Who is Who in Phylogenetic Networks (Réseaux Phylogénétiques, Phylogenetische Netzwerke, Redes Filogenéticas, Xarxes Filogenètiques, 演化網路, شبکه فیلوژنتیک)

All publications ( Html | Bibtex | Both ) Order by: Type | Year

2020

1

Katharina Huber and Guillaume Scholz. Phylogenetic networks that are their own fold-ups. In AAM, Vol. 113(101959):1-24, 2020.
Keywords: characterization, explicit network, FU-stable network, phylogenetic network, phylogeny.
Note: https://arxiv.org/abs/1804.01841.

@Article{HuberScholz2020,
AUTHOR = {Huber, Katharina and Scholz, Guillaume},
TITLE = {Phylogenetic networks that are their own fold-ups},
YEAR = {2020},
JOURNAL = {AAM},
VOLUME = {113},
NUMBER = {101959},
PAGES = {1-24},
URL = {https://doi.org/10.1016/j.aam.2019.101959},
NOTE = {https://arxiv.org/abs/1804.01841},
KEYWORDS = {characterization, explicit network, FU-stable network, phylogenetic network, phylogeny}
}

2

Andrew R. Francis, Daniel H. Huson and Mike Steel. Normalising phylogenetic networks. 2020.
Keywords: explicit network, from network, normal network, phylogenetic network, phylogeny, polynomial, Program PhyloSketch, reconstruction, tree-child network.
Note: https://arxiv.org/abs/2008.07797.

@Misc{FHS2020,
AUTHOR = {Francis, Andrew R. and Huson, Daniel H. and Steel, Mike},
TITLE = {Normalising phylogenetic networks},
YEAR = {2020},
NOTE = {https://arxiv.org/abs/2008.07797},
KEYWORDS = {explicit network, from network, normal network, phylogenetic network, phylogeny, polynomial, Program PhyloSketch, reconstruction, tree-child network}
}

3

Gabriel Cardona and Louxin Zhang. Counting and Enumerating Tree-Child Networks and Their Subclasses. In JCSS, Vol. 114:84-104, 2020.
Keywords: counting, enumeration, explicit network, galled network, galled tree, normal network, phylogenetic network, phylogeny, tree-child network.

@Article{CardonaZhang2020,
AUTHOR = {Cardona, Gabriel and Zhang, Louxin},
TITLE = {Counting and Enumerating Tree-Child Networks and Their Subclasses},
YEAR = {2020},
JOURNAL = {JCSS},
VOLUME = {114},
PAGES = {84-104},
URL = {https://doi.org/10.1016/j.jcss.2020.06.001},
KEYWORDS = {counting, enumeration, explicit network, galled network, galled tree, normal network, phylogenetic network, phylogeny, tree-child network}
}

4

Michael Fuchs, Guan-Ru Yu and Louxin Zhang. On the Asymptotic Growth of the Number of Tree-Child Networks. 2020.
Keywords: counting, explicit network, phylogenetic network, phylogeny, tree-child network.
Note: https://arxiv.org/abs/2003.08049.

@Misc{FRY2020,
AUTHOR = {Fuchs, Michael and Yu, Guan-Ru and Zhang, Louxin},
TITLE = {On the Asymptotic Growth of the Number of Tree-Child Networks},
YEAR = {2020},
NOTE = {https://arxiv.org/abs/2003.08049},
KEYWORDS = {counting, explicit network, phylogenetic network, phylogeny, tree-child network}
}

5

Louxin Zhang. Recent Progresses in the Combinatorial and Algorithmic Study of Rooted Phylogenetic Networks. In WALCOM20, Vol. 12049:22-27 of LNCS, Springer, 2020.
Keywords: cluster containment, galled network, galled tree, nearly-stable network, phylogenetic network, phylogeny, polynomial, reticulation-visible network, survey, time consistent network, tree containment, tree-based network, tree-child network.

@InProceedings{Zhang2020,
AUTHOR = {Zhang, Louxin},
TITLE = {Recent Progresses in the Combinatorial and Algorithmic Study of Rooted Phylogenetic Networks},
YEAR = {2020},
BOOKTITLE = {WALCOM20},
VOLUME = {12049},
PAGES = {22-27},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {https://doi.org/10.1007/978-3-030-39881-1_3},
KEYWORDS = {cluster containment, galled network, galled tree, nearly-stable network, phylogenetic network, phylogeny, polynomial, reticulation-visible network, survey, time consistent network, tree containment, tree-based network, tree-child network}
}

6

Andreas Gunawan, Jeyaram Rathin and Louxin Zhang. Counting and enumerating galled networks. In DAM, Vol. 283:644-654, 2020.
Keywords: counting, enumeration, explicit network, galled network, phylogenetic network, phylogeny.
Note: https://arxiv.org/abs/1812.08569.

@Article{GRZ2020,
AUTHOR = {Gunawan, Andreas and Rathin, Jeyaram and Zhang, Louxin},
TITLE = {Counting and enumerating galled networks},
YEAR = {2020},
JOURNAL = {DAM},
VOLUME = {283},
PAGES = {644-654},
URL = {https://doi.org/10.1016/j.dam.2020.03.005},
NOTE = {https://arxiv.org/abs/1812.08569},
KEYWORDS = {counting, enumeration, explicit network, galled network, phylogenetic network, phylogeny}
}

7

Marefatollah Mansouri. Counting General Phylogenetic networks. 2020.
Keywords: counting, explicit network, phylogenetic network, phylogeny.
Note: https://arxiv.org/abs/2005.14547.

@Misc{Mansouri2020b,
AUTHOR = {Mansouri, Marefatollah},
TITLE = {Counting General Phylogenetic networks},
YEAR = {2020},
NOTE = {https://arxiv.org/abs/2005.14547},
KEYWORDS = {counting, explicit network, phylogenetic network, phylogeny}
}

8

Marefatollah Mansouri. Combinatorial properties of phylogenetic networks. PhD thesis, Vienna University of Technology (Austria), Institute of Discrete Mathematics and Geometry, 2020.
Keywords: counting, explicit network, galled tree, level k phylogenetic network, normal network, phylogenetic network, phylogeny.
Note: https://dmg.tuwien.ac.at/bgitten/Theses/mansouri.pdf.

@PhdThesis{Mansouri2020,
AUTHOR = {Mansouri, Marefatollah},
TITLE = {Combinatorial properties of phylogenetic networks},
YEAR = {2020},
SCHOOL = {Vienna University of Technology (Austria), Institute of Discrete Mathematics and Geometry},
NOTE = {https://dmg.tuwien.ac.at/bgitten/Theses/mansouri.pdf},
KEYWORDS = {counting, explicit network, galled tree, level k phylogenetic network, normal network, phylogenetic network, phylogeny}
}

9

Mathilde Bouvel, Philippe Gambette and Marefatollah Mansouri. Counting Phylogenetic Networks of Level 1 and 2. In JOMB, 2020.
Keywords: counting, explicit network, level k phylogenetic network, phylogenetic network, phylogeny.
Note: https://arxiv.org/abs/1909.10460, to appear.

@Article{BGM2020,
AUTHOR = {Bouvel, Mathilde and Gambette, Philippe and Mansouri, Marefatollah},
TITLE = {Counting Phylogenetic Networks of Level 1 and 2},
YEAR = {2020},
JOURNAL = {JOMB},
NOTE = {https://arxiv.org/abs/1909.10460, to appear},
KEYWORDS = {counting, explicit network, level k phylogenetic network, phylogenetic network, phylogeny}
}

10

Jonathan Klawitter and Peter Stumpf. Drawing Tree-Based Phylogenetic Networks with Minimum Number of Crossings. 2020.
Keywords: explicit network, FPT, minimum number, NP complete, phylogenetic network, phylogeny, polynomial, visualization.
Note: https://arxiv.org/abs/2008.08960.

@Misc{KlawitterStumpf2020,
AUTHOR = {Klawitter, Jonathan and Stumpf, Peter},
TITLE = {Drawing Tree-Based Phylogenetic Networks with Minimum Number of Crossings},
YEAR = {2020},
NOTE = {https://arxiv.org/abs/2008.08960},
KEYWORDS = {explicit network, FPT, minimum number, NP complete, phylogenetic network, phylogeny, polynomial, visualization}
}

11

Elizabeth Gross, Leo van Iersel, Remie Janssen, Mark Jones, Colby Long and Yukihiro Murakami. Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes. 2020.
Keywords: characterization, distinguishability, explicit network, galled tree, phylogenetic network, population genetics, semidirected network, statistical model, uniqueness.
Note: https://arxiv.org/abs/2007.08782.

@Misc{GIJJLM2020,
AUTHOR = {Gross, Elizabeth and van Iersel, Leo and Janssen, Remie and Jones, Mark and Long, Colby and Murakami, Yukihiro},
TITLE = {Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes},
YEAR = {2020},
NOTE = {https://arxiv.org/abs/2007.08782},
KEYWORDS = {characterization, distinguishability, explicit network, galled tree, phylogenetic network, population genetics, semidirected network, statistical model, uniqueness}
}

12

Remie Janssen, Mark Jones and Yukihiro Murakami. Combining Networks Using Cherry Picking Sequences. In AlCoB20, Vol. 12099:77-92 of LNCS, Springer, 2020.
Keywords: cherry-picking, explicit network, FPT, from network, hybridization, orchard network, phylogenetic network, phylogeny, tree-child network.

@InProceedings{JJY2020,
AUTHOR = {Janssen, Remie and Jones, Mark and Murakami, Yukihiro},
TITLE = {Combining Networks Using Cherry Picking Sequences},
YEAR = {2020},
BOOKTITLE = {AlCoB20},
VOLUME = {12099},
PAGES = {77-92},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {https://doi.org/10.1007/978-3-030-42266-0_7},
KEYWORDS = {cherry-picking, explicit network, FPT, from network, hybridization, orchard network, phylogenetic network, phylogeny, tree-child network}
}

13

Hannah Brown, Lei Zuo and Dan Gusfield. Comparing Integer Linear Programming to SAT-Solving for Hard Problems in Computational and Systems Biology. In AlCoB2020, Vol. 12099:63-76 of LNCS, Springer, 2020.
Keywords: from binary characters, History bound, integer linear programming, minimum number, phylogeny, SAT.
Note: https://doi.org/10.1007/978-3-030-42266-0_6.

@InProceedings{BZG2020,
AUTHOR = {Brown, Hannah and Zuo, Lei and Gusfield, Dan},
TITLE = {Comparing Integer Linear Programming to SAT-Solving for Hard Problems in Computational and Systems Biology},
YEAR = {2020},
BOOKTITLE = {AlCoB2020},
VOLUME = {12099},
PAGES = {63-76},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {https://doi.org/10.1007/978-3-030-42266-0_6},
NOTE = {https://doi.org/10.1007/978-3-030-42266-0_6},
KEYWORDS = {from binary characters, History bound, integer linear programming, minimum number, phylogeny, SAT}
}

14

Remie Janssen and Yukihiro Murakami. Linear Time Algorithm for Tree-Child Network Containment. In AlCoB20, Vol. 12099:93-107 of LNCS, Springer, 2020.
Keywords: explicit network, from network, isomorphism, phylogenetic network, phylogeny, polynomial, reconstruction, tree-child network, tree-child sequence.
Note: https://doi.org/10.1007/978-3-030-42266-0_8.

@InProceedings{JanssenMurakami2020,
AUTHOR = {Janssen, Remie and Murakami, Yukihiro},
TITLE = {Linear Time Algorithm for Tree-Child Network Containment},
YEAR = {2020},
BOOKTITLE = {AlCoB20},
VOLUME = {12099},
PAGES = {93-107},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {https://doi.org/10.1007/978-3-030-42266-0_8},
NOTE = {https://doi.org/10.1007/978-3-030-42266-0_8},
KEYWORDS = {explicit network, from network, isomorphism, phylogenetic network, phylogeny, polynomial, reconstruction, tree-child network, tree-child sequence}
}

15

Leo van Iersel, Remie Janssen, Mark Jones, Yukihiro Murakami and Norbert Zeh. Polynomial-Time Algorithms for Phylogenetic Inference Problems Involving Duplication and Reticulation. In TCBB, Vol. 17(1):14-26, 2020.
Keywords: hybridization, minimum number, parental hybridization, phylogenetic network, phylogeny, reconstruction, weakly displaying.
Note: http://pure.tudelft.nl/ws/portalfiles/portal/71270795/08798653.pdf.

@Article{IJJMZ,
AUTHOR = {van Iersel, Leo and Janssen, Remie and Jones, Mark and Murakami, Yukihiro and Zeh, Norbert},
TITLE = {Polynomial-Time Algorithms for Phylogenetic Inference Problems Involving Duplication and Reticulation},
YEAR = {2020},
JOURNAL = {TCBB},
VOLUME = {17},
NUMBER = {1},
PAGES = {14-26},
URL = {https://doi.org/10.1109/TCBB.2019.2934957},
NOTE = {http://pure.tudelft.nl/ws/portalfiles/portal/71270795/08798653.pdf},
KEYWORDS = {hybridization, minimum number, parental hybridization, phylogenetic network, phylogeny, reconstruction, weakly displaying}
}

16

Momoko Hayamizu, Katharina Huber, Vincent Moulton and Yukihiro Murakami. Recognizing and realizing cactus metrics. In IPL, Vol. 157(105916):1-5, 2020.
Keywords: cactus graph, from distances, level k phylogenetic network, optimal realization, polynomial.
Note: https://doi.org/10.1016/j.ipl.2020.105916.

@Article{HHMM2020,
AUTHOR = {Hayamizu, Momoko and Huber, Katharina and Moulton, Vincent and Murakami, Yukihiro},
TITLE = {Recognizing and realizing cactus metrics},
YEAR = {2020},
JOURNAL = {IPL},
VOLUME = {157},
NUMBER = {105916},
PAGES = {1-5},
URL = {https://doi.org/10.1016/j.ipl.2020.105916},
NOTE = {https://doi.org/10.1016/j.ipl.2020.105916},
KEYWORDS = {cactus graph, from distances, level k phylogenetic network, optimal realization, polynomial}
}

17

Leo van Iersel, Vincent Moulton and Yukihiro Murakami. Reconstructibility of unrooted level-k phylogenetic networks from distances. In AAM, Vol. 120(102075):1-30, 2020.
Keywords: from distances, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: https://doi.org/10.1016/j.aam.2020.102075.

@Article{IMM2020,
AUTHOR = {van Iersel, Leo and Moulton, Vincent and Murakami, Yukihiro},
TITLE = {Reconstructibility of unrooted level-k phylogenetic networks from distances},
YEAR = {2020},
JOURNAL = {AAM},
VOLUME = {120},
NUMBER = {102075},
PAGES = {1-30},
URL = {https://doi.org/10.1016/j.aam.2020.102075},
NOTE = {https://doi.org/10.1016/j.aam.2020.102075},
KEYWORDS = {from distances, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction, uniqueness}
}

18

Jonathan Klawitter. The agreement distance of unrooted phylogenetic networks. In DMTCS, Vol. 21(2):22.1-23, 2020.
Keywords: agreement forest, distance between networks, explicit network, from network, phylogenetic network, phylogeny.
Note: https://dmtcs.episciences.org/6567/pdf.

@Article{Klawitter2020b,
AUTHOR = {Klawitter, Jonathan},
TITLE = {The agreement distance of unrooted phylogenetic networks},
YEAR = {2020},
JOURNAL = {DMTCS},
VOLUME = {21},
NUMBER = {2},
PAGES = {22.1-23},
URL = {https://doi.org/10.23638/DMTCS-22-1-22},
NOTE = {https://dmtcs.episciences.org/6567/pdf},
KEYWORDS = {agreement forest, distance between networks, explicit network, from network, phylogenetic network, phylogeny}
}

19

Stefan Forcey and Drew Scalzo. Phylogenetic networks as circuits with resistance distance. 2020.
Keywords: circular split system, from distances, level k phylogenetic network, NeighborNet, nested network, phylogenetic network, phylogeny, split network.
Note: https://arxiv.org/abs/2007.13574.

@Misc{ForceyScalzo2020,
AUTHOR = {Forcey, Stefan and Scalzo, Drew},
TITLE = {Phylogenetic networks as circuits with resistance distance},
YEAR = {2020},
NOTE = {https://arxiv.org/abs/2007.13574},
KEYWORDS = {circular split system, from distances, level k phylogenetic network, NeighborNet, nested network, phylogenetic network, phylogeny, split network}
}

20

Cassandra Durell and Stefan Forcey. Level-1 phylogenetic networks and their balanced minimum evolution polytopes. In JOMB, Vol. 80:1235-1263, 2020.
Keywords: from distances, galled tree, phylogenetic network, phylogeny, reconstruction, split network.
Note: https://arxiv.org/pdf/1905.09160.pdf.

@Article{DurellForcey2020,
AUTHOR = {Durell, Cassandra and Forcey, Stefan},
TITLE = {Level-1 phylogenetic networks and their balanced minimum evolution polytopes},
YEAR = {2020},
JOURNAL = {JOMB},
VOLUME = {80},
PAGES = {1235-1263},
URL = {https://doi.org/10.1007/s00285-019-01458-w},
NOTE = {https://arxiv.org/pdf/1905.09160.pdf},
KEYWORDS = {from distances, galled tree, phylogenetic network, phylogeny, reconstruction, split network}
}

21

Stefan Forcey and Drew Scalzo. Galois connections for phylogenetic networks and their polytopes. 2020.
Keywords: characterization, from distances, galled tree, planar, reconstruction, split network.
Note: https://arxiv.org/abs/2004.11944.

@Misc{ForceyScalzo2020b,
AUTHOR = {Forcey, Stefan and Scalzo, Drew},
TITLE = {Galois connections for phylogenetic networks and their polytopes},
YEAR = {2020},
NOTE = {https://arxiv.org/abs/2004.11944},
KEYWORDS = {characterization, from distances, galled tree, planar, reconstruction, split network}
}

22

Simone Linz and Charles Semple. Caterpillars on three and four leaves are sufficient to reconstruct binary normal networks. In JOMB, 2020.
Keywords: explicit network, from rooted trees, from triplets, normal network, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: https://arxiv.org/abs/2002.00483, to appear.

@Article{LinzSemple2020,
AUTHOR = {Linz, Simone and Semple, Charles},
TITLE = {Caterpillars on three and four leaves are sufficient to reconstruct binary normal networks},
YEAR = {2020},
JOURNAL = {JOMB},
URL = {https://doi.org/10.1007/s00285-020-01533-7},
NOTE = {https://arxiv.org/abs/2002.00483, to appear},
KEYWORDS = {explicit network, from rooted trees, from triplets, normal network, phylogenetic network, phylogeny, reconstruction, uniqueness}
}

23

Hadi Poormohammadi and Mohsen Sardari Zarchi. Netcombin: An algorithm for constructing optimal phylogenetic network from rooted triplets. In PLoS ONE, Vol. 15(9):e0227842.1-25, 2020.
Keywords: explicit network, from triplets, heuristic, phylogenetic network, phylogeny, Program Simplistic, Program TripNet, reconstruction.
Note: https://doi.org/10.1371/journal.pone.0227842.

@Article{PoormohammadiSardariZarchi2020,
AUTHOR = {Poormohammadi, Hadi and Sardari Zarchi, Mohsen},
TITLE = {Netcombin: An algorithm for constructing optimal phylogenetic network from rooted triplets},
YEAR = {2020},
JOURNAL = {PLoS ONE},
VOLUME = {15},
NUMBER = {9},
PAGES = {e0227842.1-25},
URL = {https://doi.org/10.1371/journal.pone.0227842},
NOTE = {https://doi.org/10.1371/journal.pone.0227842},
KEYWORDS = {explicit network, from triplets, heuristic, phylogenetic network, phylogeny, Program Simplistic, Program TripNet, reconstruction}
}

24

Hadi Poormohammadi, Mohsen Sardari Zarchi and Hossein Ghaneai. NCHB: A method for constructing rooted phylogenetic networks from rooted triplets based on height function and binarization. In JTB, Vol. 489(110144), 2020.
Keywords: explicit network, from triplets, heuristic, phylogenetic network, phylogeny, Program Simplistic, Program TripNet, reconstruction.
Note: https://doi.org/10.1016/j.jtbi.2019.110144.

@Article{PSG2020,
AUTHOR = {Poormohammadi, Hadi and Sardari Zarchi, Mohsen and Ghaneai, Hossein},
TITLE = {NCHB: A method for constructing rooted phylogenetic networks from rooted triplets based on height function and binarization},
YEAR = {2020},
JOURNAL = {JTB},
VOLUME = {489},
NUMBER = {110144},
URL = {https://doi.org/10.1016/j.jtbi.2019.110144},
NOTE = {https://doi.org/10.1016/j.jtbi.2019.110144},
KEYWORDS = {explicit network, from triplets, heuristic, phylogenetic network, phylogeny, Program Simplistic, Program TripNet, reconstruction}
}

25

Katharina Huber, Simone Linz and Vincent Moulton. Weakly displaying trees in temporal tree-child network. 2020.
Keywords: cherry-picking, from rooted trees, phylogenetic network, phylogeny, reconstruction, rigidly displaying, time consistent network, tree-child network, weakly displaying.
Note: https://arxiv.org/abs/2004.02634.

@Misc{HLM2020,
AUTHOR = {Huber, Katharina and Linz, Simone and Moulton, Vincent},
TITLE = {Weakly displaying trees in temporal tree-child network},
YEAR = {2020},
NOTE = {https://arxiv.org/abs/2004.02634},
KEYWORDS = {cherry-picking, from rooted trees, phylogenetic network, phylogeny, reconstruction, rigidly displaying, time consistent network, tree-child network, weakly displaying}
}

26

Joan Carles Pons, Celine Scornavacca and Gabriel Cardona. Generation of Level-k LGT Networks. In TCBB, Vol. 17(1):158-164, 2020.
Keywords: explicit network, level k phylogenetic network, LGT network, phylogenetic network, phylogeny.

@Article{PSC2020,
AUTHOR = {Pons, Joan Carles and Scornavacca, Celine and Cardona, Gabriel},
TITLE = {Generation of Level-k LGT Networks},
YEAR = {2020},
JOURNAL = {TCBB},
VOLUME = {17},
NUMBER = {1},
PAGES = {158-164},
URL = {https://doi.org/10.1109/TCBB.2019.2895344},
KEYWORDS = {explicit network, level k phylogenetic network, LGT network, phylogenetic network, phylogeny}
}

2019

1

Steven Kelk, Fabio Pardi, Celine Scornavacca and Leo van Iersel. Finding the most parsimonious or likely tree in a network with respect to an alignment. In JOMB, Vol. 78:527-547, 2019.
Keywords: APX hard, from network, from sequences, likelihood, NP complete, parsimony.
Note: https://arxiv.org/abs/1707.03648.

@Article{KPSI2019,
AUTHOR = {Kelk, Steven and Pardi, Fabio and Scornavacca, Celine and van Iersel, Leo},
TITLE = {Finding the most parsimonious or likely tree in a network with respect to an alignment},
YEAR = {2019},
JOURNAL = {JOMB},
VOLUME = {78},
PAGES = {527-547},
URL = {http://dx.doi.org/10.1007/s00285-018-1282-2},
NOTE = {https://arxiv.org/abs/1707.03648},
KEYWORDS = {APX hard, from network, from sequences, likelihood, NP complete, parsimony}
}

2

Joan Carles Pons, Charles Semple and Mike Steel. Tree-based networks: characterisations, metrics, and support trees. In JOMB, Vol. 78(4):899-918, 2019.
Keywords: characterization, explicit network, from network, phylogenetic network, phylogeny, time consistent network, tree-based network.
Note: https://arxiv.org/abs/1710.07836.

@Article{PSS2019,
AUTHOR = {Pons, Joan Carles and Semple, Charles and Steel, Mike},
TITLE = {Tree-based networks: characterisations, metrics, and support trees},
YEAR = {2019},
JOURNAL = {JOMB},
VOLUME = {78},
NUMBER = {4},
PAGES = {899-918},
URL = {https://doi.org/10.1007/s00285-018-1296-9},
NOTE = {https://arxiv.org/abs/1710.07836},
KEYWORDS = {characterization, explicit network, from network, phylogenetic network, phylogeny, time consistent network, tree-based network}
}

3

Katharina Huber, Vincent Moulton and Taoyang Wu. Hierarchies from lowest stable ancestors in nonbinary phylogenetic networks. In JOC, Vol. 36:200-231, 2019.
Keywords: characterization, explicit network, phylogenetic network, phylogeny.
Note: https://link.springer.com/content/pdf/10.1007/s00357-018-9279-5.pdf.

@Article{HMW2019,
AUTHOR = {Huber, Katharina and Moulton, Vincent and Wu, Taoyang},
TITLE = {Hierarchies from lowest stable ancestors in nonbinary phylogenetic networks},
YEAR = {2019},
JOURNAL = {JOC},
VOLUME = {36},
PAGES = {200-231},
NOTE = {https://link.springer.com/content/pdf/10.1007/s00357-018-9279-5.pdf},
KEYWORDS = {characterization, explicit network, phylogenetic network, phylogeny}
}

4

Simone Linz and Charles Semple. Attaching leaves and picking cherries to characterise the hybridisation number for a set of phylogenies. In AAM, Vol. 105:102-129, 2019.
Keywords: agreement forest, cherry-picking, explicit network, from rooted trees, phylogenetic network, phylogeny, reconstruction, tree-child network.
Note: https://doi.org/10.1016/j.aam.2019.01.004.

@Article{LinzSemple2019,
AUTHOR = {Linz, Simone and Semple, Charles},
TITLE = {Attaching leaves and picking cherries to characterise the hybridisation number for a set of phylogenies},
YEAR = {2019},
JOURNAL = {AAM},
VOLUME = {105},
PAGES = {102-129},
URL = {https://doi.org/10.1016/j.aam.2019.01.004},
NOTE = {https://doi.org/10.1016/j.aam.2019.01.004},
KEYWORDS = {agreement forest, cherry-picking, explicit network, from rooted trees, phylogenetic network, phylogeny, reconstruction, tree-child network}
}

5

Jonathan Klawitter. The agreement distance of rooted phylogenetic networks. In DMTCS, Vol. 21(3):19.1-24, 2019.
Keywords: agreement forest, distance between networks, explicit network, from network, phylogenetic network, phylogeny, SPR distance.
Note: https://arxiv.org/abs/1806.05800.

@Article{Klawitter2019b,
AUTHOR = {Klawitter, Jonathan},
TITLE = {The agreement distance of rooted phylogenetic networks},
YEAR = {2019},
JOURNAL = {DMTCS},
VOLUME = {21},
NUMBER = {3},
PAGES = {19.1-24},
URL = {https://doi.org/10.23638/DMTCS-21-3-19},
NOTE = {https://arxiv.org/abs/1806.05800},
KEYWORDS = {agreement forest, distance between networks, explicit network, from network, phylogenetic network, phylogeny, SPR distance}
}

6

Janosch Döcker, Leo van Iersel, Steven Kelk and Simone Linz. Deciding the existence of a cherry-picking sequence is hard on two trees. In DAM, Vol. 260:131-143, 2019.
Keywords: cherry-picking, explicit network, hybridization, minimum number, NP complete, phylogenetic network, phylogeny, reconstruction, temporal-hybridization number, time consistent network, tree-child network.
Note: https://arxiv.org/abs/1712.02965.

@Article{DIKL2019,
AUTHOR = {D{\~A}�cker, Janosch and van Iersel, Leo and Kelk, Steven and Linz, Simone},
TITLE = {Deciding the existence of a cherry-picking sequence is hard on two trees},
YEAR = {2019},
JOURNAL = {DAM},
VOLUME = {260},
PAGES = {131-143},
URL = {https://doi.org/10.1016/j.dam.2019.01.031},
NOTE = {https://arxiv.org/abs/1712.02965},
KEYWORDS = {cherry-picking, explicit network, hybridization, minimum number, NP complete, phylogenetic network, phylogeny, reconstruction, temporal-hybridization number, time consistent network, tree-child network}
}

7

Jonathan Klawitter and Simone Linz. On the Subnet Prune and Regraft Distance. In ELJC, Vol. 26(2):P2.3.1-23, 2019.
Keywords: agreement forest, explicit network, phylogenetic network, phylogeny, reticulation-visible network, SPR distance, tree-based network, tree-child network.
Note: https://arxiv.org/abs/1805.07839.

@Article{KlawitterLinz2019,
AUTHOR = {Klawitter, Jonathan and Linz, Simone},
TITLE = {On the Subnet Prune and Regraft Distance},
YEAR = {2019},
JOURNAL = {ELJC},
VOLUME = {26},
NUMBER = {2},
PAGES = {P2.3.1-23},
URL = {https://doi.org/10.37236/7860},
NOTE = {https://arxiv.org/abs/1805.07839},
KEYWORDS = {agreement forest, explicit network, phylogenetic network, phylogeny, reticulation-visible network, SPR distance, tree-based network, tree-child network}
}

8

Michael Fuchs, Bernhard Gittenberger and Marefatollah Mansouri. Counting Phylogenetic Networks with Few Reticulation Vertices: Tree-Child and Normal Networks. In Australasian Journal of Combinatorics, Vol. 73(2):385-423, 2019.
Keywords: counting, explicit network, normal network, phylogenetic network, phylogeny.
Note: https://arxiv.org/abs/1803.11325, see also erratum at https://arxiv.org/abs/2006.15784.

@Article{FGM2019,
AUTHOR = {Fuchs, Michael and Gittenberger, Bernhard and Mansouri, Marefatollah},
TITLE = {Counting Phylogenetic Networks with Few Reticulation Vertices: Tree-Child and Normal Networks},
YEAR = {2019},
JOURNAL = {Australasian Journal of Combinatorics},
VOLUME = {73},
NUMBER = {2},
PAGES = {385-423},
NOTE = {https://arxiv.org/abs/1803.11325, see also erratum at https://arxiv.org/abs/2006.15784},
KEYWORDS = {counting, explicit network, normal network, phylogenetic network, phylogeny}
}

9

Andreas Gunawan, Hongwei Yan and Louxin Zhang. Compression of Phylogenetic Networks and Algorithm for the Tree Containment Problem. In JCB, Vol. 25(3), 2019.
Keywords: explicit network, phylogenetic network, phylogeny, polynomial, quasi-reticulation-visible network, reticulation-visible network, tree containment, tree-child network.
Note: https://arxiv.org/abs/1806.07625.

@Article{GYZ2019,
AUTHOR = {Gunawan, Andreas and Yan, Hongwei and Zhang, Louxin},
TITLE = {Compression of Phylogenetic Networks and Algorithm for the Tree Containment Problem},
YEAR = {2019},
JOURNAL = {JCB},
VOLUME = {25},
NUMBER = {3},
URL = {https://doi.org/10.1089/cmb.2018.0220},
NOTE = {https://arxiv.org/abs/1806.07625},
KEYWORDS = {explicit network, phylogenetic network, phylogeny, polynomial, quasi-reticulation-visible network, reticulation-visible network, tree containment, tree-child network}
}

10

R. A. Leo Elworth, Huw A. Ogilvie, Jiafan Zhu and Luay Nakhleh. Advances in Computational Methods for Phylogenetic Networks in the Presence of Hybridization. In Tandy Warnow editor, Bioinformatics and Phylogenetics. Seminal Contributions of Bernard Moret, Vol. 29 of Computational Biology, Springer, 2019.
Keywords: explicit network, phylogenetic network, phylogeny, Program Dendroscope, Program PhyloNet, Program PhyloNetworks SNaQ, Program PIRN, Program SplitsTree, reconstruction, survey.
Note: https://bioinfocs.rice.edu/sites/g/files/bxs266/f/ElworthZhuOgilvieNakhleh.pdf

@InBook{EOZN2019,
AUTHOR = {Elworth, R. A. Leo and Ogilvie, Huw A. and Zhu, Jiafan and Nakhleh, Luay},
TITLE = {Advances in Computational Methods for Phylogenetic Networks in the Presence of Hybridization},
YEAR = {2019},
BOOKTITLE = {Bioinformatics and Phylogenetics. Seminal Contributions of Bernard Moret},
VOLUME = {29},
EDITOR = {Warnow, Tandy},
SERIES = {Computational Biology},
PUBLISHER = {Springer},
URL = {https://doi.org/10.1007/978-3-030-10837-3_13},
NOTE = {https://bioinfocs.rice.edu/sites/g/files/bxs266/f/ElworthZhuOgilvieNakhleh.pdf KEYWORDS = {explicit network, phylogenetic network, phylogeny, Program Dendroscope, Program PhyloNet, Program PhyloNetworks SNaQ, Program PIRN, Program SplitsTree, reconstruction, survey}
}

11

Louxin Zhang. Clusters, Trees, and Phylogenetic Network Classes. In Tandy Warnow editor, Bioinformatics and Phylogenetics. Seminal Contributions of Bernard Moret, Vol. 29:277-315 of Computational Biology, Springer, 2019.
Keywords: cluster containment, explicit network, phylogenetic network, phylogeny, polynomial, tree containment.

@InBook{Zhang2019,
AUTHOR = {Zhang, Louxin},
TITLE = {Clusters, Trees, and Phylogenetic Network Classes},
YEAR = {2019},
BOOKTITLE = {Bioinformatics and Phylogenetics. Seminal Contributions of Bernard Moret},
VOLUME = {29},
PAGES = {277-315},
EDITOR = {Warnow, Tandy},
SERIES = {Computational Biology},
PUBLISHER = {Springer},
URL = {https://doi.org/10.1007/978-3-030-10837-3_12},
KEYWORDS = {cluster containment, explicit network, phylogenetic network, phylogeny, polynomial, tree containment}
}

12

Louxin Zhang. Generating normal networks via leaf insertion and nearest neighbor interchange. In BMC Bioinformatics, Vol. 20(642):1-9, 2019.
Keywords: enumeration, explicit network, generation, NNI moves, phylogenetic network, phylogeny.
Note: https://link.springer.com/content/pdf/10.1186/s12859-019-3209-3.pdf.

@Article{Zhang2019b,
AUTHOR = {Zhang, Louxin},
TITLE = {Generating normal networks via leaf insertion and nearest neighbor interchange},
YEAR = {2019},
JOURNAL = {BMC Bioinformatics},
VOLUME = {20},
NUMBER = {642},
PAGES = {1-9},
URL = {https://doi.org/10.1186/s12859-019-3209-3},
NOTE = {https://link.springer.com/content/pdf/10.1186/s12859-019-3209-3.pdf},
KEYWORDS = {enumeration, explicit network, generation, NNI moves, phylogenetic network, phylogeny}
}

13

Juan Wang and Maozu Guo. IGNet: Constructing Rooted Phylogenetic Networks Based on Incompatible Graphs. In ICNC-FSKD19, Vol. 1075:894-900 of Advances in Intelligent Systems and Computing, Springer, 2019.
Keywords: explicit network, from rooted trees, phylogenetic network, phylogeny, Program BIMLR, Program IGNet, Program LNetwork, reconstruction, software.

@InProceedings{WangGuo2019,
AUTHOR = {Wang, Juan and Guo, Maozu},
TITLE = {IGNet: Constructing Rooted Phylogenetic Networks Based on Incompatible Graphs},
YEAR = {2019},
BOOKTITLE = {ICNC-FSKD19},
VOLUME = {1075},
PAGES = {894-900},
SERIES = {Advances in Intelligent Systems and Computing},
PUBLISHER = {Springer},
URL = {https://doi.org/10.1007/978-3-030-32591-6_97},
KEYWORDS = {explicit network, from rooted trees, phylogenetic network, phylogeny, Program BIMLR, Program IGNet, Program LNetwork, reconstruction, software}
}

14

Yukihiro Murakami, Leo van Iersel, Remie Janssen, Mark Jones and Vincent Moulton. Reconstructing Tree-Child Networks from Reticulate-Edge-Deleted Subnetworks. In BMB, Vol. 81:3823-3863, 2019.
Keywords: from subnetworks, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction, tree-child network, uniqueness, valid network.
Note: https://doi.org/10.1007/s11538-019-00641-w.

@Article{MIJJM,
AUTHOR = {Murakami, Yukihiro and van Iersel, Leo and Janssen, Remie and Jones, Mark and Moulton, Vincent},
TITLE = {Reconstructing Tree-Child Networks from Reticulate-Edge-Deleted Subnetworks},
YEAR = {2019},
JOURNAL = {BMB},
VOLUME = {81},
PAGES = {3823-3863},
URL = {https://doi.org/10.1007/s11538-019-00641-w},
NOTE = {https://doi.org/10.1007/s11538-019-00641-w},
KEYWORDS = {from subnetworks, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction, tree-child network, uniqueness, valid network}
}

15

Yan Hong and Juan Wang. Frin: An Efficient Method for Representing Genome Evolutionary History. In Frontiers in Genetics, Vol. 10(1261):1-8, 2019.
Keywords: explicit network, from clusters, phylogenetic network, phylogeny, Program Frin, reconstruction.
Note: https://doi.org/10.3389/fgene.2019.01261.

@Article{HongWang2019,
AUTHOR = {Hong, Yan and Wang, Juan},
TITLE = {Frin: An Efficient Method for Representing Genome Evolutionary History},
YEAR = {2019},
JOURNAL = {Frontiers in Genetics},
VOLUME = {10},
NUMBER = {1261},
PAGES = {1-8},
URL = {https://doi.org/10.3389/fgene.2019.01261},
NOTE = {https://doi.org/10.3389/fgene.2019.01261},
KEYWORDS = {explicit network, from clusters, phylogenetic network, phylogeny, Program Frin, reconstruction}
}

16

Juan Wang and Maozu Guo. A review of metrics measuring dissimilarity for rooted phylogenetic networks. In Briefings in Bioinformatics, Vol. 20(6):1972-1980, 2019.
Keywords: distance between networks, explicit network, from network, mu distance, phylogenetic network, phylogeny, survey, tree sibling network, tree-child network.

@Article{WangGuo2019b,
AUTHOR = {Wang, Juan and Guo, Maozu},
TITLE = {A review of metrics measuring dissimilarity for rooted phylogenetic networks},
YEAR = {2019},
JOURNAL = {Briefings in Bioinformatics},
VOLUME = {20},
NUMBER = {6},
PAGES = {1972-1980},
URL = {https://doi.org/10.1093/bib/bby062},
KEYWORDS = {distance between networks, explicit network, from network, mu distance, phylogenetic network, phylogeny, survey, tree sibling network, tree-child network}
}

17

Christopher Blair and Cécile Ané. Phylogenetic trees and networks can serve as powerful and complementary approaches for analysis of genomic data. In SB, Vol. 69(3):593-601, 2019.
Keywords: likelihood, phylogenetic network, phylogeny, Program PhyloNetwork, Program PhyloNetworks SNaQ, survey.

@Article{BlairAne2019,
AUTHOR = {Blair, Christopher and An{\~A}�, C{\~A}�cile},
TITLE = {Phylogenetic trees and networks can serve as powerful and complementary approaches for analysis of genomic data},
YEAR = {2019},
JOURNAL = {SB},
VOLUME = {69},
NUMBER = {3},
PAGES = {593-601},
URL = {https://doi.org/10.1093/sysbio/syz056},
KEYWORDS = {likelihood, phylogenetic network, phylogeny, Program PhyloNetwork, Program PhyloNetworks SNaQ, survey}
}

18

Péter L. Erdös, Leo van Iersel and Mark Jones. Not all phylogenetic networks are leaf-reconstructible. In JOMB, Vol. 79(5):1623-1638, 2019.
Keywords: from subnetworks, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: https://doi.org/10.1007/s00285-019-01405-9.

@Article{EIJ2019,
AUTHOR = {Erd{\~A}�s, P{\~A}�ter L. and van Iersel, Leo and Jones, Mark},
TITLE = {Not all phylogenetic networks are leaf-reconstructible},
YEAR = {2019},
JOURNAL = {JOMB},
VOLUME = {79},
NUMBER = {5},
PAGES = {1623-1638},
URL = {https://doi.org/10.1007/s00285-019-01405-9},
NOTE = {https://doi.org/10.1007/s00285-019-01405-9},
KEYWORDS = {from subnetworks, phylogenetic network, phylogeny, reconstruction, uniqueness}
}

19

Konstantinos Mampentzidis. Comparison and Construction of Phylogenetic Trees and Networks. PhD thesis, Aarhus University, Denmark, 2019.
Keywords: distance between networks, explicit network, from network, phylogenetic network, phylogeny, polynomial, triplet distance.
Note: https://pure.au.dk/ws/files/172250681/thesis_Konstantinos_Mampentzidis.pdf.

@PhdThesis{Mampentzidis2019,
AUTHOR = {Mampentzidis, Konstantinos},
TITLE = {Comparison and Construction of Phylogenetic Trees and Networks},
YEAR = {2019},
SCHOOL = {Aarhus University, Denmark},
URL = {https://pure.au.dk/ws/files/172250681/thesis_Konstantinos_Mampentzidis.pdf},
NOTE = {https://pure.au.dk/ws/files/172250681/thesis_Konstantinos_Mampentzidis.pdf},
KEYWORDS = {distance between networks, explicit network, from network, phylogenetic network, phylogeny, polynomial, triplet distance}
}

20

Jesper Jansson, Konstantinos Mampentzidis, Ramesh Rajaby and Wing-Kin Sung. Computing the Rooted Triplet Distance Between Phylogenetic Networks. In IWOCA19, Vol. 11638:290-303 of LNCS, Springer, 2019.
Keywords: distance between networks, from network, phylogenetic network, phylogeny, polynomial, triplet distance.

@InProceedings{JMS2019,
AUTHOR = {Jansson, Jesper and Mampentzidis, Konstantinos and Rajaby, Ramesh and Sung, Wing-Kin},
TITLE = {Computing the Rooted Triplet Distance Between Phylogenetic Networks},
YEAR = {2019},
BOOKTITLE = {IWOCA19},
VOLUME = {11638},
PAGES = {290-303},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {https://doi.org/10.1007/978-3-030-25005-8_24},
KEYWORDS = {distance between networks, from network, phylogenetic network, phylogeny, polynomial, triplet distance}
}

21

Janosch Döcker, Simone Linz and Charles Semple. Displaying trees across two phylogenetic networks. In TCS, Vol. 796:129-146, 2019.
Keywords: display set, explicit network, normal network, phylogenetic network, phylogeny, time consistent network, tree-child network.
Note: https://arxiv.org/abs/1901.06612.

@Article{DLS2019,
AUTHOR = {D{\~A}�cker, Janosch and Linz, Simone and Semple, Charles},
TITLE = {Displaying trees across two phylogenetic networks},
YEAR = {2019},
JOURNAL = {TCS},
VOLUME = {796},
PAGES = {129-146},
URL = {https://doi.org/10.1016/j.tcs.2019.09.003},
NOTE = {https://arxiv.org/abs/1901.06612},
KEYWORDS = {display set, explicit network, normal network, phylogenetic network, phylogeny, time consistent network, tree-child network}
}

22

Katharina Huber, Leo van Iersel, Remie Janssen, Mark Jones, Vincent Moulton, Yukihiro Murakami and Charles Semple. Rooting for phylogenetic networks. 2019.
Keywords: explicit network, from network, level k phylogenetic network, orchard network, orientation, phylogenetic network, phylogeny, reconstruction, stack-free network, tree-based network, tree-child network, valid network.
Note: https://arxiv.org/abs/1906.07430.

@Misc{HIJJMMS2019,
AUTHOR = {Huber, Katharina and van Iersel, Leo and Janssen, Remie and Jones, Mark and Moulton, Vincent and Murakami, Yukihiro and Semple, Charles},
TITLE = {Rooting for phylogenetic networks},
YEAR = {2019},
NOTE = {https://arxiv.org/abs/1906.07430},
KEYWORDS = {explicit network, from network, level k phylogenetic network, orchard network, orientation, phylogenetic network, phylogeny, reconstruction, stack-free network, tree-based network, tree-child network, valid network}
}

23

Gabriel Cardona, Joan Carles Pons and Celine Scornavacca. Generation of Binary Tree-Child phylogenetic networks. In PLoS Computational Biology, Vol. 15(10):e1007440.1-29, 2019.
Keywords: enumeration, explicit network, generation, phylogenetic network, phylogeny, Program PhyloNetwork, Program TCGenerators, software, tree-child network.
Note: https://doi.org/10.1371/journal.pcbi.1007440.

@Article{CPS2019,
AUTHOR = {Cardona, Gabriel and Pons, Joan Carles and Scornavacca, Celine},
TITLE = {Generation of Binary Tree-Child phylogenetic networks},
YEAR = {2019},
JOURNAL = {PLoS Computational Biology},
VOLUME = {15},
NUMBER = {10},
PAGES = {e1007440.1-29},
URL = {https://doi.org/10.1371/journal.pcbi.1007440},
NOTE = {https://doi.org/10.1371/journal.pcbi.1007440},
KEYWORDS = {enumeration, explicit network, generation, phylogenetic network, phylogeny, Program PhyloNetwork, Program TCGenerators, software, tree-child network}
}

2018

1

Leo van Iersel, Steven Kelk, Giorgios Stamoulis, Leen Stougie and Olivier Boes. On unrooted and root-uncertain variants of several well-known phylogenetic network problems. In ALG, Vol. 80(11):2993-3022, 2018.
Keywords: explicit network, FPT, from network, from unrooted trees, NP complete, phylogenetic network, phylogeny, reconstruction, tree containment.
Note: https://hal.inria.fr/hal-01599716.

@Article{IKSSB2018,
AUTHOR = {van Iersel, Leo and Kelk, Steven and Stamoulis, Giorgios and Stougie, Leen and Boes, Olivier},
TITLE = {On unrooted and root-uncertain variants of several well-known phylogenetic network problems},
YEAR = {2018},
JOURNAL = {ALG},
VOLUME = {80},
NUMBER = {11},
PAGES = {2993-3022},
URL = {https://doi.org/10.1007/s00453-017-0366-5},
NOTE = {https://hal.inria.fr/hal-01599716},
KEYWORDS = {explicit network, FPT, from network, from unrooted trees, NP complete, phylogenetic network, phylogeny, reconstruction, tree containment}
}

2

Laura Jetten and Leo van Iersel. Nonbinary tree-based phylogenetic networks. In TCBB, Vol. 15(1):205-217, 2018.
Keywords: characterization, explicit network, phylogenetic network, phylogeny, tree-based network.
Note: http://arxiv.org/abs/1601.04974.

@Article{JettenIersel2018,
AUTHOR = {Jetten, Laura and van Iersel, Leo},
TITLE = {Nonbinary tree-based phylogenetic networks},
YEAR = {2018},
JOURNAL = {TCBB},
VOLUME = {15},
NUMBER = {1},
PAGES = {205-217},
URL = {http://dx.doi.org/10.1109/TCBB.2016.2615918},
NOTE = {http://arxiv.org/abs/1601.04974},
KEYWORDS = {characterization, explicit network, phylogenetic network, phylogeny, tree-based network}
}

3

Daniel H. Huson and Simone Linz. Autumn Algorithm - Computation of Hybridization Networks for Realistic Phylogenetic Trees. In TCBB, Vol. 15:398-410, 2018.
Keywords: explicit network, from rooted trees, phylogenetic network, phylogeny, Program Dendroscope, reconstruction.
Note: https://simonelinz.files.wordpress.com/2016/06/hl16.pdf.

@Article{HusonLinz2018,
AUTHOR = {Huson, Daniel H. and Linz, Simone},
TITLE = {Autumn Algorithm - Computation of Hybridization Networks for Realistic Phylogenetic Trees},
YEAR = {2018},
JOURNAL = {TCBB},
VOLUME = {15},
PAGES = {398-410},
URL = {http://dx.doi.org/10.1109/TCBB.2016.2537326},
NOTE = {https://simonelinz.files.wordpress.com/2016/06/hl16.pdf},
KEYWORDS = {explicit network, from rooted trees, phylogenetic network, phylogeny, Program Dendroscope, reconstruction}
}

4

Andrew R. Francis, Charles Semple and Mike Steel. New characterisations of tree-based networks and proximity measures. In Advances in Applied Mathematics, Vol. 93:93-107, 2018.
Keywords: characterization, explicit network, phylogenetic network, phylogeny, time consistent network, tree-based network.
Note: https://arxiv.org/abs/1611.04225.

@Article{FSS2018,
AUTHOR = {Francis, Andrew R. and Semple, Charles and Steel, Mike},
TITLE = {New characterisations of tree-based networks and proximity measures},
YEAR = {2018},
JOURNAL = {Advances in Applied Mathematics},
VOLUME = {93},
PAGES = {93-107},
URL = {http://doi.org/10.1016/j.aam.2017.08.003},
NOTE = {https://arxiv.org/abs/1611.04225},
KEYWORDS = {characterization, explicit network, phylogenetic network, phylogeny, time consistent network, tree-based network}
}

5

Mathias Weller. Linear-Time Tree Containment in Phylogenetic Networks. In RECOMB-CG18, Vol. 11183:309-323 of LNCS, Springer, 2018.
Keywords: explicit network, from network, from rooted trees, nearly-stable network, phylogenetic network, phylogeny, polynomial, reconstruction, reticulation-visible network, tree containment.
Note: https://arxiv.org/abs/1702.06364.

@InProceedings{Weller2018,
AUTHOR = {Weller, Mathias},
TITLE = {Linear-Time Tree Containment in Phylogenetic Networks},
YEAR = {2018},
BOOKTITLE = {RECOMB-CG18},
VOLUME = {11183},
PAGES = {309-323},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {https://doi.org/10.1007/978-3-030-00834-5_18},
NOTE = {https://arxiv.org/abs/1702.06364},
KEYWORDS = {explicit network, from network, from rooted trees, nearly-stable network, phylogenetic network, phylogeny, polynomial, reconstruction, reticulation-visible network, tree containment}
}

6

Andrew R. Francis, Katharina Huber, Vincent Moulton and Taoyang Wu. Bounds for phylogenetic network space metrics. In JOMB, Vol. 76(5):1229-1248, 2018.
Keywords: bound, distance between networks, from network, NNI distance, NNI moves, phylogenetic network, phylogeny, SPR distance, TBR distance.
Note: https://arxiv.org/abs/1702.05609.

@Article{FHMW2018,
AUTHOR = {Francis, Andrew R. and Huber, Katharina and Moulton, Vincent and Wu, Taoyang},
TITLE = {Bounds for phylogenetic network space metrics},
YEAR = {2018},
JOURNAL = {JOMB},
VOLUME = {76},
NUMBER = {5},
PAGES = {1229-1248},
URL = {https://dx.doi.org/10.1007/s00285-017-1171-0},
NOTE = {https://arxiv.org/abs/1702.05609},
KEYWORDS = {bound, distance between networks, from network, NNI distance, NNI moves, phylogenetic network, phylogeny, SPR distance, TBR distance}
}

7

Hussein A. Hejase, Natalie VandePol, Gregory A. Bonito and Kevin J. Liu. Fast and accurate statistical inference of phylogenetic networks using large-scale genomic sequence data. In RECOMB-CG18, Vol. 11183:242-259 of LNCS, Springer, 2018.
Keywords: explicit network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program FastNet, reconstruction.
Note: http://biorxiv.org/content/early/2017/05/01/132795.

@InProceedings{HVBL2018,
AUTHOR = {Hejase, Hussein A. and VandePol, Natalie and Bonito, Gregory A. and Liu, Kevin J.},
TITLE = {Fast and accurate statistical inference of phylogenetic networks using large-scale genomic sequence data},
YEAR = {2018},
BOOKTITLE = {RECOMB-CG18},
VOLUME = {11183},
PAGES = {242-259},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {https://doi.org/10.1007/978-3-030-00834-5_14},
NOTE = {http://biorxiv.org/content/early/2017/05/01/132795},
KEYWORDS = {explicit network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program FastNet, reconstruction}
}

8

Andrew R. Francis, Katharina Huber and Vincent Moulton. Tree-based unrooted phylogenetic networks. In BMB, Vol. 80(2):404-416, 2018.
Keywords: characterization, explicit network, NP complete, phylogenetic network, phylogeny, tree containment, tree-based network, unrooted tree-based network.
Note: https://arxiv.org/abs/1704.02062.

@Article{FHM2018,
AUTHOR = {Francis, Andrew R. and Huber, Katharina and Moulton, Vincent},
TITLE = {Tree-based unrooted phylogenetic networks},
YEAR = {2018},
JOURNAL = {BMB},
VOLUME = {80},
NUMBER = {2},
PAGES = {404-416},
URL = {https://doi.org/10.1007/s11538-017-0381-3},
NOTE = {https://arxiv.org/abs/1704.02062},
KEYWORDS = {characterization, explicit network, NP complete, phylogenetic network, phylogeny, tree containment, tree-based network, unrooted tree-based network}
}

9

Magnus Bordewich, Charles Semple and Nihan Tokac. Constructing tree-child networks from distance matrices. In Algorithmica, Vol. 80(8):2240-2259, 2018.
Keywords: compressed network, explicit network, from distances, phylogenetic network, phylogeny, polynomial, reconstruction, tree-child network, uniqueness.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BSN17.pdf.

@Article{BST2018,
AUTHOR = {Bordewich, Magnus and Semple, Charles and Tokac, Nihan},
TITLE = {Constructing tree-child networks from distance matrices},
YEAR = {2018},
JOURNAL = {Algorithmica},
VOLUME = {80},
NUMBER = {8},
PAGES = {2240-2259},
URL = {http://dx.doi.org/10.1007/s00453-017-0320-6},
NOTE = {http://www.math.canterbury.ac.nz/~c.semple/papers/BSN17.pdf},
KEYWORDS = {compressed network, explicit network, from distances, phylogenetic network, phylogeny, polynomial, reconstruction, tree-child network, uniqueness}
}

10

Andreas Gunawan. Solving the Tree Containment Problem for Reticulation-visible Networks in Linear Time. In AlCoB18, Vol. 10849:24-36 of LNCS, Springer, 2018.
Keywords: explicit network, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulation-visible network, tree containment.
Note: https://arxiv.org/abs/1702.04088.

@InProceedings{Gunawan2018,
AUTHOR = {Gunawan, Andreas},
TITLE = {Solving the Tree Containment Problem for Reticulation-visible Networks in Linear Time},
YEAR = {2018},
BOOKTITLE = {AlCoB18},
VOLUME = {10849},
PAGES = {24-36},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {https://doi.org/10.1007/978-3-319-91938-6_3},
NOTE = {https://arxiv.org/abs/1702.04088},
KEYWORDS = {explicit network, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulation-visible network, tree containment}
}

11

Philippe Gambette, Andreas Gunawan, Anthony Labarre, Stéphane Vialette and Louxin Zhang. Solving the Tree Containment Problem in Linear Time for Nearly Stable Phylogenetic Networks. In DAM, Vol. 246:62-79, 2018.
Keywords: explicit network, from network, from rooted trees, nearly-stable network, phylogenetic network, phylogeny, polynomial, tree containment.
Note: https://hal-upec-upem.archives-ouvertes.fr/hal-01575001/en/.

@Article{GGLVZ2018,
AUTHOR = {Gambette, Philippe and Gunawan, Andreas and Labarre, Anthony and Vialette, St{\~A}�phane and Zhang, Louxin},
TITLE = {Solving the Tree Containment Problem in Linear Time for Nearly Stable Phylogenetic Networks},
YEAR = {2018},
JOURNAL = {DAM},
VOLUME = {246},
PAGES = {62-79},
URL = {http://dx.doi.org/10.1016/j.dam.2017.07.015},
NOTE = {https://hal-upec-upem.archives-ouvertes.fr/hal-01575001/en/},
KEYWORDS = {explicit network, from network, from rooted trees, nearly-stable network, phylogenetic network, phylogeny, polynomial, tree containment}
}

12

Remie Janssen, Mark Jones, Péter L. Erdös, Leo van Iersel and Celine Scornavacca. Exploring the tiers of rooted phylogenetic network space using tail moves. In BMB, Vol. 80(8):2177-2208, 2018.
Keywords: distance between networks, explicit network, from network, NNI moves, orientation, phylogenetic network, phylogeny, SPR distance.
Note: https://arxiv.org/abs/1708.07656.

@Article{JJEIS2018,
AUTHOR = {Janssen, Remie and Jones, Mark and Erd{\~A}�s, P{\~A}�ter L. and van Iersel, Leo and Scornavacca, Celine},
TITLE = {Exploring the tiers of rooted phylogenetic network space using tail moves},
YEAR = {2018},
JOURNAL = {BMB},
VOLUME = {80},
NUMBER = {8},
PAGES = {2177-2208},
URL = {http://dx.doi.org/10.1007/s11538-018-0452-0},
NOTE = {https://arxiv.org/abs/1708.07656},
KEYWORDS = {distance between networks, explicit network, from network, NNI moves, orientation, phylogenetic network, phylogeny, SPR distance}
}

13

Jonathan Klawitter. The SNPR neighbourhood of tree-child networks. In JGAA, Vol. 22(2):329-355, 2018.
Keywords: distance between networks, phylogenetic network, phylogeny, SPR distance, tree-child network.
Note: https://arxiv.org/abs/1707.09579

@Article{Klawitter2018b,
AUTHOR = {Klawitter, Jonathan},
TITLE = {The SNPR neighbourhood of tree-child networks},
YEAR = {2018},
JOURNAL = {JGAA},
VOLUME = {22},
NUMBER = {2},
PAGES = {329-355},
URL = {http://dx.doi.org/10.7155/jgaa.00472},
NOTE = {https://arxiv.org/abs/1707.09579 KEYWORDS = {distance between networks, phylogenetic network, phylogeny, SPR distance, tree-child network}
}

14

Sarah Bastkowski, Daniel Mapleson, Andreas Spillner, Taoyang Wu, Monika Balvociute and Vincent Moulton. SPECTRE: a Suite of PhylogEnetiC Tools for Reticulate Evolution. In BIO, Vol. 34(6):1057-1058, 2018.
Keywords: abstract network, NeighborNet, phylogenetic network, phylogeny, Program FlatNJ, Program QNet, Program SplitsTree, reconstruction, software, split network.
Note: https://doi.org/10.1101/169177.

@Article{BMSWBM2018,
AUTHOR = {Bastkowski, Sarah and Mapleson, Daniel and Spillner, Andreas and Wu, Taoyang and Balvociute, Monika and Moulton, Vincent},
TITLE = {SPECTRE: a Suite of PhylogEnetiC Tools for Reticulate Evolution},
YEAR = {2018},
JOURNAL = {BIO},
VOLUME = {34},
NUMBER = {6},
PAGES = {1057-1058},
URL = {https://doi.org/10.1093/bioinformatics/btx740},
NOTE = {https://doi.org/10.1101/169177},
KEYWORDS = {abstract network, NeighborNet, phylogenetic network, phylogeny, Program FlatNJ, Program QNet, Program SplitsTree, reconstruction, software, split network}
}

15

Sebastien Roch and Kun-Chieh Wang. Circular Networks from Distorted Metrics. In RECOMB18, Vol. 10812:167-176 of LNCS, Springer, 2018.
Keywords: abstract network, circular split system, from distances, NeighborNet, phylogenetic network, phylogeny, reconstruction, split network.
Note: https://arxiv.org/abs/1707.05722.

@InProceedings{RW2018,
AUTHOR = {Roch, Sebastien and Wang, Kun-Chieh},
TITLE = {Circular Networks from Distorted Metrics},
YEAR = {2018},
BOOKTITLE = {RECOMB18},
VOLUME = {10812},
PAGES = {167-176},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {https://doi.org/10.1007/978-3-319-89929-9_11},
NOTE = {https://arxiv.org/abs/1707.05722},
KEYWORDS = {abstract network, circular split system, from distances, NeighborNet, phylogenetic network, phylogeny, reconstruction, split network}
}

16

Paul Bastide, Claudia Solís-Lemus, Ricardo Kriebel, Kenneth William Sparks and Cécile Ané. Phylogenetic Comparative Methods on Phylogenetic Networks with Reticulations. In SB, Vol. 67(5):800-820, 2018.
Keywords: ancestral trait reconstruction, from network, likelihood, Program PhyloNetworks SNaQ, software, statistical model, statistical test.
Note: https://doi.org/10.1101/194050.

@Article{BSKSA2018,
AUTHOR = {Bastide, Paul and Sol{\~A}�s-Lemus, Claudia and Kriebel, Ricardo and Sparks, Kenneth William and An{\~A}�, C{\~A}�cile},
TITLE = {Phylogenetic Comparative Methods on Phylogenetic Networks with Reticulations},
YEAR = {2018},
JOURNAL = {SB},
VOLUME = {67},
NUMBER = {5},
PAGES = {800-820},
URL = {http://dx.doi.org/10.1093/sysbio/syy033},
NOTE = {https://doi.org/10.1101/194050},
KEYWORDS = {ancestral trait reconstruction, from network, likelihood, Program PhyloNetworks SNaQ, software, statistical model, statistical test}
}

17

Katharina Huber, Vincent Moulton, Charles Semple and Taoyang Wu. Quarnet inference rules for level-1 networks. In BMB, Vol. 80:2137-2153, 2018.
Keywords: explicit network, from quarnets, from subnetworks, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction.
Note: https://arxiv.org/abs/1711.06720.

@Article{HMSW2018,
AUTHOR = {Huber, Katharina and Moulton, Vincent and Semple, Charles and Wu, Taoyang},
TITLE = {Quarnet inference rules for level-1 networks},
YEAR = {2018},
JOURNAL = {BMB},
VOLUME = {80},
PAGES = {2137-2153},
URL = {https://doi.org/10.1007/s11538-018-0450-2},
NOTE = {https://arxiv.org/abs/1711.06720},
KEYWORDS = {explicit network, from quarnets, from subnetworks, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction}
}

18

Leo van Iersel and Vincent Moulton. Leaf-reconstructibility of phylogenetic networks. In SIAM Journal on Discrete Mathematics, Vol. 32(3):2047-2066, 2018.
Keywords: explicit network, from network, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: https://arxiv.org/abs/1701.08982.

@Article{IerselMoulton2018,
AUTHOR = {van Iersel, Leo and Moulton, Vincent},
TITLE = {Leaf-reconstructibility of phylogenetic networks},
YEAR = {2018},
JOURNAL = {SIAM Journal on Discrete Mathematics},
VOLUME = {32},
NUMBER = {3},
PAGES = {2047-2066},
URL = {https://dx.doi.org/10.1137/17M1111930},
NOTE = {https://arxiv.org/abs/1701.08982},
KEYWORDS = {explicit network, from network, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction, uniqueness}
}

19

Kristina Wicke and Mareike Fischer. Phylogenetic diversity and biodiversity indices on phylogenetic networks. In MB, Vol. 298:80-90, 2018.
Keywords: diversity, explicit network, from network, normal network, phylogenetic network, phylogeny.
Note: https://arxiv.org/abs/1706.05279.

@Article{WickeFischer2018,
AUTHOR = {Wicke, Kristina and Fischer, Mareike},
TITLE = {Phylogenetic diversity and biodiversity indices on phylogenetic networks},
YEAR = {2018},
JOURNAL = {MB},
VOLUME = {298},
PAGES = {80-90},
URL = {https://doi.org/10.1016/j.mbs.2018.02.005},
NOTE = {https://arxiv.org/abs/1706.05279},
KEYWORDS = {diversity, explicit network, from network, normal network, phylogenetic network, phylogeny}
}

20

Magnus Bordewich and Charles Semple. A universal tree-based network with the minimum number of reticulations. In DAM, Vol. 250:357-362, 2018.
Keywords: explicit network, phylogenetic network, phylogeny, tree-based network.
Note: https://arxiv.org/abs/1707.08274.

@Article{BordewichSemple2018b,
AUTHOR = {Bordewich, Magnus and Semple, Charles},
TITLE = {A universal tree-based network with the minimum number of reticulations},
YEAR = {2018},
JOURNAL = {DAM},
VOLUME = {250},
PAGES = {357-362},
URL = {https://doi.org/10.1016/j.dam.2018.05.010},
NOTE = {https://arxiv.org/abs/1707.08274},
KEYWORDS = {explicit network, phylogenetic network, phylogeny, tree-based network}
}

21

Janosch Döcker and Simone Linz. On the existence of a cherry-picking sequence. In TCS, Vol. 714:36-50, 2018.
Keywords: cherry-picking, explicit network, from rooted trees, NP complete, phylogenetic network, phylogeny, reconstruction, temporal-hybridization number, time consistent network, tree-child network.
Note: https://arxiv.org/abs/1712.04127.

@Article{DöckerLinz2018,
AUTHOR = {D{\~A}�cker, Janosch and Linz, Simone},
TITLE = {On the existence of a cherry-picking sequence},
YEAR = {2018},
JOURNAL = {TCS},
VOLUME = {714},
PAGES = {36-50},
URL = {https://doi.org/10.1016/j.tcs.2017.12.005},
NOTE = {https://arxiv.org/abs/1712.04127},
KEYWORDS = {cherry-picking, explicit network, from rooted trees, NP complete, phylogenetic network, phylogeny, reconstruction, temporal-hybridization number, time consistent network, tree-child network}
}

22

Elizabeth Gross and Colby Long. Distinguishing Phylogenetic Networks. In SIAM Journal on Applied Algebra and Geometry, Vol. 2(1):72-93, 2018.
Keywords: distinguishability, phylogenetic network, phylogeny, semidirected network, statistical model, uniqueness.
Note: https://arxiv.org/abs/1706.03060.

@Article{GrossLong2018,
AUTHOR = {Gross, Elizabeth and Long, Colby},
TITLE = {Distinguishing Phylogenetic Networks},
YEAR = {2018},
JOURNAL = {SIAM Journal on Applied Algebra and Geometry},
VOLUME = {2},
NUMBER = {1},
PAGES = {72-93},
URL = {https://doi.org/10.1137/17M1134238},
NOTE = {https://arxiv.org/abs/1706.03060},
KEYWORDS = {distinguishability, phylogenetic network, phylogeny, semidirected network, statistical model, uniqueness}
}

23

James H. Degnan. Modeling Hybridization Under the Network Multispecies Coalescent. In SB, Vol. 67(5):786-799, 2018.
Keywords: distance between networks, phylogenetic network, phylogeny, reconstruction, survey.
Note: https://academic.oup.com/sysbio/article/67/5/786/5017269.

@Article{Degnan2018,
AUTHOR = {Degnan, James H.},
TITLE = {Modeling Hybridization Under the Network Multispecies Coalescent},
YEAR = {2018},
JOURNAL = {SB},
VOLUME = {67},
NUMBER = {5},
PAGES = {786-799},
URL = {https://doi.org/10.1093/sysbio/syy040},
NOTE = {https://academic.oup.com/sysbio/article/67/5/786/5017269},
KEYWORDS = {distance between networks, phylogenetic network, phylogeny, reconstruction, survey}
}

24

Andrew R. Francis and Vincent Moulton. Identifiability of tree-child phylogenetic networks under a probabilistic recombination-mutation model of evolution. In JTB, Vol. 446:160-167, 2018.
Keywords: explicit network, from unrooted trees, phylogenetic network, phylogeny, tree-child network, uniqueness.
Note: https://arxiv.org/abs/1712.04223.

@Article{FrancisMoulton2018,
AUTHOR = {Francis, Andrew R. and Moulton, Vincent},
TITLE = {Identifiability of tree-child phylogenetic networks under a probabilistic recombination-mutation model of evolution},
YEAR = {2018},
JOURNAL = {JTB},
VOLUME = {446},
PAGES = {160-167},
URL = {https://doi.org/10.1016/j.jtbi.2018.03.011},
NOTE = {https://arxiv.org/abs/1712.04223},
KEYWORDS = {explicit network, from unrooted trees, phylogenetic network, phylogeny, tree-child network, uniqueness}
}

25

Leo van Iersel, Mark Jones and Celine Scornavacca. Improved maximum parsimony models for phylogenetic networks. In SB, Vol. 67(3):518-542, 2018.
Keywords: explicit network, FPT, from sequences, NP complete, parsimony, phylogenetic network, phylogeny, reconstruction, weakly displaying.
Note: https://leovaniersel.files.wordpress.com/2017/12/improved_parsimony_networks.pdf.

@Article{IJS2018,
AUTHOR = {van Iersel, Leo and Jones, Mark and Scornavacca, Celine},
TITLE = {Improved maximum parsimony models for phylogenetic networks},
YEAR = {2018},
JOURNAL = {SB},
VOLUME = {67},
NUMBER = {3},
PAGES = {518-542},
URL = {https://dx.doi.org/10.1093/sysbio/syx094},
NOTE = {https://leovaniersel.files.wordpress.com/2017/12/improved_parsimony_networks.pdf},
KEYWORDS = {explicit network, FPT, from sequences, NP complete, parsimony, phylogenetic network, phylogeny, reconstruction, weakly displaying}
}

26

Sajad Mirzaei. Efficient Algorithms for Trees and Networks in Evolutionary Genomics. PhD thesis, University of Connecticut, 2018.
Keywords: branch length, explicit network, haplotype network, heuristic, Program PIRN, reconstruction.
Note: https://opencommons.uconn.edu/dissertations/1853.

@PhdThesis{Sajad2018,
AUTHOR = {Mirzaei, Sajad},
TITLE = {Efficient Algorithms for Trees and Networks in Evolutionary Genomics},
YEAR = {2018},
SCHOOL = {University of Connecticut},
URL = {https://opencommons.uconn.edu/dissertations/1853},
NOTE = {https://opencommons.uconn.edu/dissertations/1853},
KEYWORDS = {branch length, explicit network, haplotype network, heuristic, Program PIRN, reconstruction}
}

27

Charles Semple and Jack Simpson. When is a phylogenetic network simply an amalgamation of two trees? In BMB, Vol. 80(9):2338-2348, 2018.
Keywords: characterization, phylogenetic network, phylogeny, reticulation-visible network, stack-free network, tree-based network.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/SS18.pdf.

@Article{SempleSimpson2018,
AUTHOR = {Semple, Charles and Simpson, Jack},
TITLE = {When is a phylogenetic network simply an amalgamation of two trees?},
YEAR = {2018},
JOURNAL = {BMB},
VOLUME = {80},
NUMBER = {9},
PAGES = {2338-2348},
URL = {https://doi.org/10.1007/s11538-018-0463-x},
NOTE = {http://www.math.canterbury.ac.nz/~c.semple/papers/SS18.pdf},
KEYWORDS = {characterization, phylogenetic network, phylogeny, reticulation-visible network, stack-free network, tree-based network}
}

28

Magnus Bordewich, Katharina Huber, Vincent Moulton and Charles Semple. Recovering normal networks from shortest inter-taxa distance information. In JOMB, Vol. 77(3):571-594, 2018.
Keywords: explicit network, from distances, normal network, phylogenetic network, phylogeny, polynomial, reconstruction, uniqueness.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BHMS18.pdf.

@Article{BHMS2018,
AUTHOR = {Bordewich, Magnus and Huber, Katharina and Moulton, Vincent and Semple, Charles},
TITLE = {Recovering normal networks from shortest inter-taxa distance information},
YEAR = {2018},
JOURNAL = {JOMB},
VOLUME = {77},
NUMBER = {3},
PAGES = {571-594},
URL = {http://dx.doi.org/10.1007/s00285-018-1218-x},
NOTE = {http://www.math.canterbury.ac.nz/~c.semple/papers/BHMS18.pdf},
KEYWORDS = {explicit network, from distances, normal network, phylogenetic network, phylogeny, polynomial, reconstruction, uniqueness}
}

29

Chi Zhang, Huw A. Ogilvie, Alexei J. Drummond and Tanja Stadler. Bayesian Inference of Species Networks from Multilocus Sequence Data. In MBE, Vol. 35(2):504-517, 2018.
Keywords: bayesian, explicit network, from sequences, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: https://dx.doi.org/10.1093/molbev/msx307.

@Article{ZODT2018,
AUTHOR = {Zhang, Chi and Ogilvie, Huw A. and Drummond, Alexei J. and Stadler, Tanja},
TITLE = {Bayesian Inference of Species Networks from Multilocus Sequence Data},
YEAR = {2018},
JOURNAL = {MBE},
VOLUME = {35},
NUMBER = {2},
PAGES = {504-517},
URL = {https://dx.doi.org/10.1093/molbev/msx307},
NOTE = {https://dx.doi.org/10.1093/molbev/msx307},
KEYWORDS = {bayesian, explicit network, from sequences, phylogenetic network, phylogeny, reconstruction, statistical model}
}

30

Guillaume Scholz. New algorithms and mathematical tools for phylogenetics beyond trees. PhD thesis, University of East Anglia, 2018.
Keywords: circular split system, explicit network, explicit network, from splits, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction, split network, uniqueness.
Note: https://ueaeprints.uea.ac.uk/id/eprint/66952.

@PhdThesis{Scholz2018,
AUTHOR = {Scholz, Guillaume},
TITLE = {New algorithms and mathematical tools for phylogenetics beyond trees},
YEAR = {2018},
SCHOOL = {University of East Anglia},
NOTE = { https://ueaeprints.uea.ac.uk/id/eprint/66952},
KEYWORDS = {circular split system, explicit network, explicit network, from splits, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction, split network, uniqueness}
}

31

Kuang-Yu Chang, Yun Cui, Siu-Ming Yiu and Wing-Kai Hon. Reconstructing One-Articulated Networks with Distance Matrices. In JCB, Vol. 25(3):253-269, 2018.
Keywords: explicit network, from distances, k-reticulated, phylogenetic network, phylogeny, reconstruction.

@Article{CCYH2018,
AUTHOR = {Chang, Kuang-Yu and Cui, Yun and Yiu, Siu-Ming and Hon, Wing-Kai},
TITLE = {Reconstructing One-Articulated Networks with Distance Matrices},
YEAR = {2018},
JOURNAL = {JCB},
VOLUME = {25},
NUMBER = {3},
PAGES = {253-269},
URL = {http://dx.doi.org/10.1089/cmb.2017.0148},
KEYWORDS = {explicit network, from distances, k-reticulated, phylogenetic network, phylogeny, reconstruction}
}

32

Kuang-Yu Chang, Wing-Kai Hon and Sharma V. Thankachan. Compact Encoding for Galled-Trees and its Applications. In 2018 Data Compression Conference, Pages 297-306, 2018.
Keywords: compression, counting, explicit network, galled tree, phylogenetic network, polynomial.

@InProceedings{CHT2018,
AUTHOR = {Chang, Kuang-Yu and Hon, Wing-Kai and Thankachan, Sharma V.},
TITLE = {Compact Encoding for Galled-Trees and its Applications},
YEAR = {2018},
BOOKTITLE = {2018 Data Compression Conference},
PAGES = {297-306},
URL = {http://dx.doi.org/10.1109/DCC.2018.00038},
KEYWORDS = {compression, counting, explicit network, galled tree, phylogenetic network, polynomial}
}

33

Hongwei Yan, Andreas Gunawan and Louxin Zhang. S-Cluster++: a fast program for solving the cluster containment problem for phylogenetic networks. In BIO, Vol. 34(17):i680–i686, 2018.
Keywords: cluster containment, explicit network, phylogenetic network, phylogeny, SAT.
Note: http://dx.doi.org/10.1093/bioinformatics/bty594.

@Article{YGZ2018,
AUTHOR = {Yan, Hongwei and Gunawan, Andreas and Zhang, Louxin},
TITLE = {S-Cluster++: a fast program for solving the cluster containment problem for phylogenetic networks},
YEAR = {2018},
JOURNAL = {BIO},
VOLUME = {34},
NUMBER = {17},
PAGES = {i680{\^a}��i686},
URL = {http://dx.doi.org/10.1093/bioinformatics/bty594},
NOTE = {http://dx.doi.org/10.1093/bioinformatics/bty594},
KEYWORDS = {cluster containment, explicit network, phylogenetic network, phylogeny, SAT}
}

34

Michael Hendriksen. Tree-based unrooted nonbinary phylogenetic networks. In MBIO, Vol. 302:131-138, 2018.
Keywords: characterization, phylogenetic network, phylogeny, tree-based network, unrooted tree-based network.

@Article{Hendriksen2018,
AUTHOR = {Hendriksen, Michael},
TITLE = {Tree-based unrooted nonbinary phylogenetic networks},
YEAR = {2018},
JOURNAL = {MBIO},
VOLUME = {302},
PAGES = {131-138},
URL = {http://dx.doi.org/10.1016/j.mbs.2018.06.005},
KEYWORDS = {characterization, phylogenetic network, phylogeny, tree-based network, unrooted tree-based network}
}

35

Dingqiao Wen, Yun Yu, Jiafan Zhu and Luay Nakhleh. Inferring Phylogenetic Networks Using PhyloNet. In SB, Vol. 67(4):735-740, 2018.
Keywords: bayesian, likelihood, parsimony, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, software.

@Article{WYZN2018,
AUTHOR = {Wen, Dingqiao and Yu, Yun and Zhu, Jiafan and Nakhleh, Luay},
TITLE = {Inferring Phylogenetic Networks Using PhyloNet},
YEAR = {2018},
JOURNAL = {SB},
VOLUME = {67},
NUMBER = {4},
PAGES = {735-740},
URL = {http://dx.doi.org/10.1093/sysbio/syy015},
KEYWORDS = {bayesian, likelihood, parsimony, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, software}
}

36

Jiafan Zhu, Dingqiao Wen, Yun Yu, Heidi M. Meudt and Luay Nakhleh. Bayesian inference of phylogenetic networks from bi-allelic genetic markers. In PLoS Computational Biology, Vol. 14(1):e1005932.1-32, 2018.
Keywords: bayesian, explicit network, from multistate characters, phylogenetic network, phylogeny, Program PhyloNet.
Note: https://doi.org/10.1371/journal.pcbi.1005932.

@Article{ZWYMN2018,
AUTHOR = {Zhu, Jiafan and Wen, Dingqiao and Yu, Yun and Meudt, Heidi M. and Nakhleh, Luay},
TITLE = {Bayesian inference of phylogenetic networks from bi-allelic genetic markers},
YEAR = {2018},
JOURNAL = {PLoS Computational Biology},
VOLUME = {14},
NUMBER = {1},
PAGES = {e1005932.1-32},
URL = {https://doi.org/10.1371/journal.pcbi.1005932},
NOTE = {https://doi.org/10.1371/journal.pcbi.1005932},
KEYWORDS = {bayesian, explicit network, from multistate characters, phylogenetic network, phylogeny, Program PhyloNet}
}

37

Dingqiao Wen and Luay Nakhleh. Coestimating Reticulate Phylogenies and Gene Trees from Multilocus Sequence Data. In SB, Vol. 67(3):439-457, 2018.
Keywords: bayesian, explicit network, from sequences, incomplete lineage sorting, phylogenetic network, phylogeny, Program PhyloNet, reconstruction.
Note: https://doi.org/10.1093/sysbio/syx085.

@Article{WenNakhleh2018,
AUTHOR = {Wen, Dingqiao and Nakhleh, Luay},
TITLE = {Coestimating Reticulate Phylogenies and Gene Trees from Multilocus Sequence Data},
YEAR = {2018},
JOURNAL = {SB},
VOLUME = {67},
NUMBER = {3},
PAGES = {439-457},
URL = {https://doi.org/10.1093/sysbio/syx085},
NOTE = {https://doi.org/10.1093/sysbio/syx085},
KEYWORDS = {bayesian, explicit network, from sequences, incomplete lineage sorting, phylogenetic network, phylogeny, Program PhyloNet, reconstruction}
}

38

Andreas Gunawan. On the tree and cluster containment problems for phylogenetic networks. PhD thesis, National University of Singapore, 2018.
Keywords: cluster containment, explicit network, galled network, genetically stable network, nearly-stable network, phylogenetic network, phylogeny, reticulation-visible network, tree containment.
Note: https://scholarbank.nus.edu.sg/handle/10635/144270.

@PhdThesis{Gunawan2018b,
AUTHOR = {Gunawan, Andreas},
TITLE = {On the tree and cluster containment problems for phylogenetic networks},
YEAR = {2018},
SCHOOL = {National University of Singapore},
URL = {https://scholarbank.nus.edu.sg/handle/10635/144270},
NOTE = {https://scholarbank.nus.edu.sg/handle/10635/144270},
KEYWORDS = {cluster containment, explicit network, galled network, genetically stable network, nearly-stable network, phylogenetic network, phylogeny, reticulation-visible network, tree containment}
}

39

Leo van Iersel, Remie Janssen, Mark Jones, Yukihiro Murakami and Norbert Zeh. Polynomial-Time Algorithms for Phylogenetic Inference Problems. In AlCoB18, Vol. 10849:37-49 of LNCS, Springer, 2018.
Keywords: hybridization, minimum number, parental hybridization, phylogenetic network, phylogeny, polynomial, reconstruction, weakly displaying.
Note: https://research.tudelft.nl/files/53686721/10.1007_978_3_319_91938_6_4.pdf.

@InProceedings{IJJYZ2018,
AUTHOR = {van Iersel, Leo and Janssen, Remie and Jones, Mark and Murakami, Yukihiro and Zeh, Norbert},
TITLE = {Polynomial-Time Algorithms for Phylogenetic Inference Problems},
YEAR = {2018},
BOOKTITLE = {AlCoB18},
VOLUME = {10849},
PAGES = {37-49},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {https://doi.org/10.1007/978-3-319-91938-6_4},
NOTE = {https://research.tudelft.nl/files/53686721/10.1007_978_3_319_91938_6_4.pdf},
KEYWORDS = {hybridization, minimum number, parental hybridization, phylogenetic network, phylogeny, polynomial, reconstruction, weakly displaying}
}

2017

1

Katharina Huber, Leo van Iersel, Vincent Moulton, Celine Scornavacca and Taoyang Wu. Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets. In ALG, Vol. 77(1):173-200, 2017.
Keywords: explicit network, FPT, from binets, from subnetworks, from trinets, NP complete, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://arxiv.org/abs/1411.6804.

@Article{HIMSW2017,
AUTHOR = {Huber, Katharina and van Iersel, Leo and Moulton, Vincent and Scornavacca, Celine and Wu, Taoyang},
TITLE = {Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets},
YEAR = {2017},
JOURNAL = {ALG},
VOLUME = {77},
NUMBER = {1},
PAGES = {173-200},
URL = {http://dx.doi.org/10.1007/s00453-015-0069-8},
NOTE = {http://arxiv.org/abs/1411.6804},
KEYWORDS = {explicit network, FPT, from binets, from subnetworks, from trinets, NP complete, phylogenetic network, phylogeny, polynomial, reconstruction}
}

2

Christopher Bryant, Mareike Fischer, Simone Linz and Charles Semple. On the Quirks of Maximum Parsimony and Likelihood on Phylogenetic Networks. In JTB, Vol. 417:100-108, 2017.
Keywords: explicit network, from sequences, likelihood, parsimony, phylogenetic network, phylogeny.
Note: http://arxiv.org/abs/1505.06898.

@Article{BFLS2017,
AUTHOR = {Bryant, Christopher and Fischer, Mareike and Linz, Simone and Semple, Charles},
TITLE = {On the Quirks of Maximum Parsimony and Likelihood on Phylogenetic Networks},
YEAR = {2017},
JOURNAL = {JTB},
VOLUME = {417},
PAGES = {100-108},
URL = {http://dx.doi.org/10.1016/j.jtbi.2017.01.013},
NOTE = {http://arxiv.org/abs/1505.06898},
KEYWORDS = {explicit network, from sequences, likelihood, parsimony, phylogenetic network, phylogeny}
}

3

Monika Balvociute, David Bryant and Andreas Spillner. When can splits be drawn in the plane? In SIAM Journal on Discrete Mathematics, Vol. 31(2):839-856, 2017.
Keywords: abstract network, characterization, flat, phylogenetic network, planar, split, split network.
Note: http://arxiv.org/abs/1509.06104v1.

@Article{BBS2017,
AUTHOR = {Balvociute, Monika and Bryant, David and Spillner, Andreas},
TITLE = {When can splits be drawn in the plane?},
YEAR = {2017},
JOURNAL = {SIAM Journal on Discrete Mathematics},
VOLUME = {31},
NUMBER = {2},
PAGES = {839-856},
URL = {http://dx.doi.org/10.1137/15M1040852},
NOTE = {http://arxiv.org/abs/1509.06104v1},
KEYWORDS = {abstract network, characterization, flat, phylogenetic network, planar, split, split network}
}

4

Satyan L. Devadoss and Samantha Petti. A Space of Phylogenetic Networks. In SIAM Journal on Applied Algebra and Geometry, Vol. 1(1):683-705, 2017.
Keywords: abstract network, circular split system, phylogenetic network, phylogeny, split network.
Note: http://arxiv.org/abs/1607.06978.

@Article{DevadossPetti2017,
AUTHOR = {Devadoss, Satyan L. and Petti, Samantha},
TITLE = {A Space of Phylogenetic Networks},
YEAR = {2017},
JOURNAL = {SIAM Journal on Applied Algebra and Geometry},
VOLUME = {1},
NUMBER = {1},
PAGES = {683-705},
URL = {https://dx.doi.org/10.1137/16M1103129},
NOTE = {http://arxiv.org/abs/1607.06978},
KEYWORDS = {abstract network, circular split system, phylogenetic network, phylogeny, split network}
}

5

Charles Semple. Size of a phylogenetic network. In DAM, Vol. 217(2):362-367, 2017.
Keywords: compressed network, number of vertices, phylogenetic network, phylogeny, stack-free network.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/S16.pdf.

@Article{Semple2017,
AUTHOR = {Semple, Charles},
TITLE = {Size of a phylogenetic network},
YEAR = {2017},
JOURNAL = {DAM},
VOLUME = {217},
NUMBER = {2},
PAGES = {362-367},
URL = {http://dx.doi.org/10.1016/j.dam.2016.09.004},
NOTE = {http://www.math.canterbury.ac.nz/~c.semple/papers/S16.pdf},
KEYWORDS = {compressed network, number of vertices, phylogenetic network, phylogeny, stack-free network}
}

6

Philippe Gambette, Katharina Huber and Steven Kelk. On the challenge of reconstructing level-1 phylogenetic networks from triplets and clusters. In JOMB, Vol. 74(7):1729-1751, 2017.
Keywords: from clusters, from triplets, galled tree, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: http://dx.doi.org/10.1007/s00285-016-1068-3.

@Article{GHK2017,
AUTHOR = {Gambette, Philippe and Huber, Katharina and Kelk, Steven},
TITLE = {On the challenge of reconstructing level-1 phylogenetic networks from triplets and clusters},
YEAR = {2017},
JOURNAL = {JOMB},
VOLUME = {74},
NUMBER = {7},
PAGES = {1729-1751},
URL = {http://dx.doi.org/10.1007/s00285-016-1068-3},
NOTE = {http://dx.doi.org/10.1007/s00285-016-1068-3},
KEYWORDS = {from clusters, from triplets, galled tree, phylogenetic network, phylogeny, reconstruction, uniqueness}
}

7

Philippe Gambette, Katharina Huber and Guillaume Scholz. Uprooted Phylogenetic Networks. In BMB, Vol. 79(9):2022-2048, 2017.
Keywords: circular split system, explicit network, from splits, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction, split network, uniqueness.
Note: http://arxiv.org/abs/1511.08387.

@Article{GHS2017,
AUTHOR = {Gambette, Philippe and Huber, Katharina and Scholz, Guillaume},
TITLE = {Uprooted Phylogenetic Networks},
YEAR = {2017},
JOURNAL = {BMB},
VOLUME = {79},
NUMBER = {9},
PAGES = {2022-2048},
URL = {http://dx.doi.org/10.1007/s11538-017-0318-x},
NOTE = {http://arxiv.org/abs/1511.08387},
KEYWORDS = {circular split system, explicit network, from splits, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction, split network, uniqueness}
}

8

Julia Matsieva, Steven Kelk, Celine Scornavacca, Chris Whidden and Dan Gusfield. A Resolution of the Static Formulation Question for the Problem of Computing the History Bound. In TCBB, Vol. 14(2):404-417, 2017.
Keywords: ARG, explicit network, from sequences, minimum number, phylogenetic network, phylogeny.

@Article{MKSWG2017,
AUTHOR = {Matsieva, Julia and Kelk, Steven and Scornavacca, Celine and Whidden, Chris and Gusfield, Dan},
TITLE = {A Resolution of the Static Formulation Question for the Problem of Computing the History Bound},
YEAR = {2017},
JOURNAL = {TCBB},
VOLUME = {14},
NUMBER = {2},
PAGES = {404-417},
URL = {http://dx.doi.org/10.1109/TCBB.2016.2527645},
KEYWORDS = {ARG, explicit network, from sequences, minimum number, phylogenetic network, phylogeny}
}

9

Sha Zhu and James H. Degnan. Displayed Trees Do Not Determine Distinguishability Under the Network Multispecies Coalescent. In SB, Vol. 66(2):283-298, 2017.
Keywords: branch length, coalescent, explicit network, from network, likelihood, phylogenetic network, phylogeny, Program Hybrid-coal, Program Hybrid-Lambda, Program PhyloNet, software, uniqueness.
Note: presentation available at https://www.youtube.com/watch?v=JLYGTfEZG7g.

@Article{ShaDegnan2017,
AUTHOR = {Zhu, Sha and Degnan, James H.},
TITLE = {Displayed Trees Do Not Determine Distinguishability Under the Network Multispecies Coalescent},
YEAR = {2017},
JOURNAL = {SB},
VOLUME = {66},
NUMBER = {2},
PAGES = {283-298},
URL = {http://dx.doi.org/10.1093/sysbio/syw097},
NOTE = {presentation available at https://www.youtube.com/watch?v=JLYGTfEZG7g},
KEYWORDS = {branch length, coalescent, explicit network, from network, likelihood, phylogenetic network, phylogeny, Program Hybrid-coal, Program Hybrid-Lambda, Program PhyloNet, software, uniqueness}
}

10

Misagh Kordi and Mukul S. Bansal. On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees. In TCBB, Vol. 14(3):587-599, 2017.
Keywords: duplication, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: http://compbio.engr.uconn.edu/papers/Kordi_DTLreconciliationPreprint2015.pdf.

@Article{KordiBansal2017,
AUTHOR = {Kordi, Misagh and Bansal, Mukul S.},
TITLE = {On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees},
YEAR = {2017},
JOURNAL = {TCBB},
VOLUME = {14},
NUMBER = {3},
PAGES = {587-599},
URL = {http://dx.doi.org/10.1109/TCBB.2015.2511761},
NOTE = {http://compbio.engr.uconn.edu/papers/Kordi_DTLreconciliationPreprint2015.pdf},
KEYWORDS = {duplication, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction}
}

11

Andreas Gunawan, Bhaskar DasGupta and Louxin Zhang. A decomposition theorem and two algorithms for reticulation-visible networks. In Information and Computation, Vol. 252:161-175, 2017.
Keywords: cluster containment, explicit network, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulation-visible network, tree containment.
Note: https://www.cs.uic.edu/~dasgupta/resume/publ/papers/Infor_Comput_IC4848_final.pdf.

@Article{GDZ2017,
AUTHOR = {Gunawan, Andreas and DasGupta, Bhaskar and Zhang, Louxin},
TITLE = {A decomposition theorem and two algorithms for reticulation-visible networks},
YEAR = {2017},
JOURNAL = {Information and Computation},
VOLUME = {252},
PAGES = {161-175},
URL = {http://dx.doi.org/10.1016/j.ic.2016.11.001},
NOTE = {https://www.cs.uic.edu/~dasgupta/resume/publ/papers/Infor_Comput_IC4848_final.pdf},
KEYWORDS = {cluster containment, explicit network, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulation-visible network, tree containment}
}

12

Gabriel Cardona and Joan Carles Pons. Reconstruction of LGT networks from tri-LGT-nets. In JOMB, Vol. 75(6-7):1669-1692, 2017.
Keywords: explicit network, from subnetworks, from tri-LGT-nets, LGT network, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: https://doi.org/10.1007/s00285-017-1171-0.

@Article{CardonaPons2017,
AUTHOR = {Cardona, Gabriel and Pons, Joan Carles},
TITLE = {Reconstruction of LGT networks from tri-LGT-nets},
YEAR = {2017},
JOURNAL = {JOMB},
VOLUME = {75},
NUMBER = {6-7},
PAGES = {1669-1692},
URL = {http://dx.doi.org/10.1007/s00285-017-1131-8},
NOTE = {https://doi.org/10.1007/s00285-017-1171-0},
KEYWORDS = {explicit network, from subnetworks, from tri-LGT-nets, LGT network, phylogenetic network, phylogeny, reconstruction, uniqueness}
}

13

Bingxin Lu, Louxin Zhang and Hon Wai Leong. A program to compute the soft Robinson-Foulds distance between phylogenetic networks. In APBC17, Vol. 18(Suppl. 2):111 of BMC Genomics, 2017.
Keywords: cluster containment, distance between networks, explicit network, exponential algorithm, from network, phylogenetic network, phylogeny, Program icelu-PhyloNetwork.
Note: http://dx.doi.org/10.1186/s12864-017-3500-5.

@InProceedings{LZL2017,
AUTHOR = {Lu, Bingxin and Zhang, Louxin and Leong, Hon Wai},
TITLE = {A program to compute the soft Robinson-Foulds distance between phylogenetic networks},
YEAR = {2017},
BOOKTITLE = {APBC17},
VOLUME = {18},
NUMBER = {Suppl. 2},
PAGES = {111},
SERIES = {BMC Genomics},
URL = {http://dx.doi.org/10.1186/s12864-017-3500-5},
NOTE = {http://dx.doi.org/10.1186/s12864-017-3500-5},
KEYWORDS = {cluster containment, distance between networks, explicit network, exponential algorithm, from network, phylogenetic network, phylogeny, Program icelu-PhyloNetwork}
}

14

Vincent Moulton, James Oldman and Taoyang Wu. A cubic-time algorithm for computing the trinet distance between level-1 networks. In IPL, Vol. 123:36-41, 2017.
Keywords: distance between networks, explicit network, from network, phylogenetic network, phylogeny, polynomial, Program TriLoNet.
Note: https://doi.org/10.1016/j.ipl.2017.03.002.

@Article{MOW2017,
AUTHOR = {Moulton, Vincent and Oldman, James and Wu, Taoyang},
TITLE = {A cubic-time algorithm for computing the trinet distance between level-1 networks},
YEAR = {2017},
JOURNAL = {IPL},
VOLUME = {123},
PAGES = {36-41},
URL = {https://doi.org/10.1016/j.ipl.2017.03.002},
NOTE = {https://doi.org/10.1016/j.ipl.2017.03.002},
KEYWORDS = {distance between networks, explicit network, from network, phylogenetic network, phylogeny, polynomial, Program TriLoNet}
}

15

Olga K. Kamneva and Noah A. Rosenberg. Simulation-Based Evaluation of Hybridization Network Reconstruction Methods in the Presence of Incomplete Lineage Sorting. In Evolutionary Bioinformatics, Vol. 13(1176934317691935):1-16, 2017.
Keywords: evaluation, explicit network, incomplete lineage sorting, simulation.
Note: https://dx.doi.org/10.1177%2F1176934317691935.

@Article{KamnevaRosenberg2017,
AUTHOR = {Kamneva, Olga K. and Rosenberg, Noah A.},
TITLE = {Simulation-Based Evaluation of Hybridization Network Reconstruction Methods in the Presence of Incomplete Lineage Sorting},
YEAR = {2017},
JOURNAL = {Evolutionary Bioinformatics},
VOLUME = {13},
NUMBER = {1176934317691935},
PAGES = {1-16},
URL = {https://dx.doi.org/10.1177%2F1176934317691935},
NOTE = {https://dx.doi.org/10.1177%2F1176934317691935},
KEYWORDS = {evaluation, explicit network, incomplete lineage sorting, simulation}
}

16

Magnus Bordewich, Simone Linz and Charles Semple. Lost in space? Generalising subtree prune and regraft to spaces of phylogenetic networks. In JTB, Vol. 423:1-12, 2017.
Keywords: distance between networks, explicit network, phylogenetic network, phylogeny, reticulation-visible network, SPR distance, tree-based network, tree-child network.
Note: https://simonelinz.files.wordpress.com/2017/04/bls171.pdf.

@Article{BLS2017,
AUTHOR = {Bordewich, Magnus and Linz, Simone and Semple, Charles},
TITLE = {Lost in space? Generalising subtree prune and regraft to spaces of phylogenetic networks},
YEAR = {2017},
JOURNAL = {JTB},
VOLUME = {423},
PAGES = {1-12},
URL = {https://doi.org/10.1016/j.jtbi.2017.03.032},
NOTE = {https://simonelinz.files.wordpress.com/2017/04/bls171.pdf},
KEYWORDS = {distance between networks, explicit network, phylogenetic network, phylogeny, reticulation-visible network, SPR distance, tree-based network, tree-child network}
}

17

Celine Scornavacca, Joan Carles Pons and Gabriel Cardona. Fast algorithm for the reconciliation of gene trees and LGT networks. In JTB, Vol. 418:129-137, 2017.
Keywords: duplication, explicit network, from network, from rooted trees, lateral gene transfer, LGT network, loss, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction.

@Article{SPC2017,
AUTHOR = {Scornavacca, Celine and Pons, Joan Carles and Cardona, Gabriel},
TITLE = {Fast algorithm for the reconciliation of gene trees and LGT networks},
YEAR = {2017},
JOURNAL = {JTB},
VOLUME = {418},
PAGES = {129-137},
URL = {https://doi.org/10.1016/j.jtbi.2017.01.024},
KEYWORDS = {duplication, explicit network, from network, from rooted trees, lateral gene transfer, LGT network, loss, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction}
}

18

Jesper Jansson, Ramesh Rajaby and Wing-Kin Sung. An Efficient Algorithm for the Rooted Triplet Distance Between Galled Trees. In AlCoB17, Vol. 10252:115-126 of LNCS, Springer, 2017.
Keywords: distance between networks, from network, phylogenetic network, phylogeny, polynomial, reconstruction, triplet distance.
Note: .

@InProceedings{JRS2017,
AUTHOR = {Jansson, Jesper and Rajaby, Ramesh and Sung, Wing-Kin},
TITLE = {An Efficient Algorithm for the Rooted Triplet Distance Between Galled Trees},
YEAR = {2017},
BOOKTITLE = {AlCoB17},
VOLUME = {10252},
PAGES = {115-126},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {http://dx.doi.org/10.1007/978-3-319-58163-7_8},
NOTE = {},
KEYWORDS = {distance between networks, from network, phylogenetic network, phylogeny, polynomial, reconstruction, triplet distance}
}

19

Leo van Iersel, Vincent Moulton, Eveline De Swart and Taoyang Wu. Binets: fundamental building blocks for phylogenetic networks. In BMB, Vol. 79(5):1135-1154, 2017.
Keywords: approximation, explicit network, from binets, from subnetworks, galled tree, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1007/s11538-017-0275-4.

@Article{IMSW2017,
AUTHOR = {van Iersel, Leo and Moulton, Vincent and De Swart, Eveline and Wu, Taoyang},
TITLE = {Binets: fundamental building blocks for phylogenetic networks},
YEAR = {2017},
JOURNAL = {BMB},
VOLUME = {79},
NUMBER = {5},
PAGES = {1135-1154},
URL = {http://dx.doi.org/10.1007/s11538-017-0275-4},
NOTE = {http://dx.doi.org/10.1007/s11538-017-0275-4},
KEYWORDS = {approximation, explicit network, from binets, from subnetworks, galled tree, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, reconstruction}
}

20

Juan Wang and Maozu Guo. A Metric on the Space of kth-order reduced Phylogenetic Networks. In Scientific Reports, Vol. 7(3189):1-10, 2017.
Keywords: distance between networks, explicit network, from network, kth-order reduced network, phylogenetic network, phylogeny, polynomial.
Note: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5466651/.

@Article{WangGuo2017,
AUTHOR = {Wang, Juan and Guo, Maozu},
TITLE = {A Metric on the Space of kth-order reduced Phylogenetic Networks},
YEAR = {2017},
JOURNAL = {Scientific Reports},
VOLUME = {7},
NUMBER = {3189},
PAGES = {1-10},
URL = {https://dx.doi.org/10.1038/s41598-017-03363-y},
NOTE = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5466651/},
KEYWORDS = {distance between networks, explicit network, from network, kth-order reduced network, phylogenetic network, phylogeny, polynomial}
}

21

Philippe Gambette, Leo van Iersel, Mark Jones, Manuel Lafond, Fabio Pardi and Celine Scornavacca. Rearrangement Moves on Rooted Phylogenetic Networks. In PLoS Computational Biology, Vol. 13(8):e1005611.1-21, 2017.
Keywords: distance between networks, explicit network, from network, NNI distance, NNI moves, phylogenetic network, phylogeny, SPR distance.
Note: https://hal-upec-upem.archives-ouvertes.fr/hal-01572624/en/.

@Article{GIJLPS2017,
AUTHOR = {Gambette, Philippe and van Iersel, Leo and Jones, Mark and Lafond, Manuel and Pardi, Fabio and Scornavacca, Celine},
TITLE = {Rearrangement Moves on Rooted Phylogenetic Networks},
YEAR = {2017},
JOURNAL = {PLoS Computational Biology},
VOLUME = {13},
NUMBER = {8},
PAGES = {e1005611.1-21},
URL = {http://dx.doi.org/10.1371/journal.pcbi.1005611},
NOTE = {https://hal-upec-upem.archives-ouvertes.fr/hal-01572624/en/},
KEYWORDS = {distance between networks, explicit network, from network, NNI distance, NNI moves, phylogenetic network, phylogeny, SPR distance}
}

22

Han Lai, Maureen Stolzer and Dannie Durand. Fast Heuristics for Resolving Weakly Supported Branches Using Duplication, Transfers, and Losses. In RECOMB-CG17, Vol. 10562:298-320 of LNCS, Springer, 2017.
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program Notung, reconstruction.

@InProceedings{LSD2017,
AUTHOR = {Lai, Han and Stolzer, Maureen and Durand, Dannie},
TITLE = {Fast Heuristics for Resolving Weakly Supported Branches Using Duplication, Transfers, and Losses},
YEAR = {2017},
BOOKTITLE = {RECOMB-CG17},
VOLUME = {10562},
PAGES = {298-320},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {http://dx.doi.org/10.1007/978-3-319-67979-2_16},
KEYWORDS = {duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program Notung, reconstruction}
}

23

Claudia Solís-Lemus, Paul Bastide and Cécile Ané. PhyloNetworks: A Package for Phylogenetic Networks. In MBE, Vol. 34(12):3292-3298, 2017.
Keywords: from sequences, from trees, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, reconstruction, software.
Note: https://doi.org/10.1093/molbev/msx235.

@Article{CBA2017,
AUTHOR = {Sol{\~A}�s-Lemus, Claudia and Bastide, Paul and An{\~A}�, C{\~A}�cile},
TITLE = {PhyloNetworks: A Package for Phylogenetic Networks},
YEAR = {2017},
JOURNAL = {MBE},
VOLUME = {34},
NUMBER = {12},
PAGES = {3292-3298},
URL = {http://dx.doi.org/10.1093/molbev/msx235},
NOTE = {https://doi.org/10.1093/molbev/msx235},
KEYWORDS = {from sequences, from trees, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, reconstruction, software}
}

24

Ruzbeh Tusserkani, Hadi Poormohammadi, Azin Azadi and Changiz Eslahchi. Inferring phylogenies from minimal information. In AEEICB17, Pages 202-206, IEEE, 2017.
Keywords: from triplets, phylogenetic network, phylogeny, Program TripNet, reconstruction.

@InProceedings{TPAE2017,
AUTHOR = {Tusserkani, Ruzbeh and Poormohammadi, Hadi and Azadi, Azin and Eslahchi, Changiz},
TITLE = {Inferring phylogenies from minimal information},
YEAR = {2017},
BOOKTITLE = {AEEICB17},
PAGES = {202-206},
PUBLISHER = {IEEE},
URL = {https://doi.org/10.1109/AEEICB.2017.7972412},
KEYWORDS = {from triplets, phylogenetic network, phylogeny, Program TripNet, reconstruction}
}

25

Klaus Schliep, Alastair J. Potts, David A. Morrison and Guido W. Grimm. Intertwining phylogenetic trees and networks. In Methods in Ecology and Evolution, Vol. 8(10):1212-1220, 2017.
Keywords: abstract network, from network, from unrooted trees, phylogenetic network, phylogeny, split network, visualization.
Note: http://dx.doi.org/10.1111/2041-210X.12760.

@Article{KPMG2017,
AUTHOR = {Schliep, Klaus and Potts, Alastair J. and Morrison, David A. and Grimm, Guido W.},
TITLE = {Intertwining phylogenetic trees and networks},
YEAR = {2017},
JOURNAL = {Methods in Ecology and Evolution},
VOLUME = {8},
NUMBER = {10},
PAGES = {1212-1220},
NOTE = {http://dx.doi.org/10.1111/2041-210X.12760},
KEYWORDS = {abstract network, from network, from unrooted trees, phylogenetic network, phylogeny, split network, visualization}
}

26

Timothy G. Vaughan. IcyTree: rapid browser-based visualization for phylogenetic trees and networks. In BIO, Vol. 33(15):2392-2394, 2017.
Keywords: ARG, explicit network, from network, phylogenetic network, phylogeny, Program IcyTree, software, visualization.
Note: http://dx.doi.org/10.1093/bioinformatics/btx155.

@Article{Vaughan2017,
AUTHOR = {Vaughan, Timothy G.},
TITLE = {IcyTree: rapid browser-based visualization for phylogenetic trees and networks},
YEAR = {2017},
JOURNAL = {BIO},
VOLUME = {33},
NUMBER = {15},
PAGES = {2392-2394},
URL = {http://dx.doi.org/10.1093/bioinformatics/btx155},
NOTE = {http://dx.doi.org/10.1093/bioinformatics/btx155},
KEYWORDS = {ARG, explicit network, from network, phylogenetic network, phylogeny, Program IcyTree, software, visualization}
}

27

Mohammad Hossein Reyhani and Hadi Poormohammadi. RPNCH: A Method for Constructing Rooted Phylogenetic Networks from Rooted Triplets based on Height Function. In Archives of Advances in Biosciences, Vol. 8(4):14-20, 2017.
Keywords: explicit network, from triplets, heuristic, phylogenetic network, phylogeny, reconstruction.
Note: http://journals.sbmu.ac.ir/jps/article/view/16707.

@Article{ReyhaniPoormohammadi2017,
AUTHOR = {Reyhani, Mohammad Hossein and Poormohammadi, Hadi},
TITLE = {RPNCH: A Method for Constructing Rooted Phylogenetic Networks from Rooted Triplets based on Height Function},
YEAR = {2017},
JOURNAL = {Archives of Advances in Biosciences},
VOLUME = {8},
NUMBER = {4},
PAGES = {14-20},
URL = {https://doi.org/10.22037/jps.v8i4.16707},
NOTE = {http://journals.sbmu.ac.ir/jps/article/view/16707},
KEYWORDS = {explicit network, from triplets, heuristic, phylogenetic network, phylogeny, reconstruction}
}

28

Hussein A. Hejase. Scalable Phylogenetic Analysis and Functional Interpretation of Genomes with Complex Evolutionary Histories. PhD thesis, Michigan State University, 2017.
Keywords: explicit network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program FastNet, reconstruction.
Note: https://dx.doi.org/10.25335/M5T855.

@PhdThesis{Hejase2017,
AUTHOR = {Hejase, Hussein A.},
TITLE = {Scalable Phylogenetic Analysis and Functional Interpretation of Genomes with Complex Evolutionary Histories},
YEAR = {2017},
SCHOOL = {Michigan State University},
URL = {http://dx.doi.org/10.25335/M5T855},
NOTE = {https://dx.doi.org/10.25335/M5T855},
KEYWORDS = {explicit network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program FastNet, reconstruction}
}

29

Edwin Jacox, Mathias Weller, Eric Tannier and Celine Scornavacca. Resolution and reconciliation of non-binary gene trees with transfers, duplications and losses. In BIO, Vol. 33(7):980-987, 2017.
Keywords: duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1093/bioinformatics/btw778.

@Article{JWTS2017,
AUTHOR = {Jacox, Edwin and Weller, Mathias and Tannier, Eric and Scornavacca, Celine},
TITLE = {Resolution and reconciliation of non-binary gene trees with transfers, duplications and losses},
YEAR = {2017},
JOURNAL = {BIO},
VOLUME = {33},
NUMBER = {7},
PAGES = {980-987},
URL = {http://dx.doi.org/10.1093/bioinformatics/btw778},
NOTE = {http://dx.doi.org/10.1093/bioinformatics/btw778},
KEYWORDS = {duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction}
}

30

Luay Nakhleh. Phylogenetic Networks: From Displayed Trees to a Distribution of Gene Trees. Phyloseminar #70, 2017.
Keywords: bayesian, coalescent, explicit network, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, statistical model.
Note: https://www.youtube.com/watch?v=dkQsvLUUDcQ.

@Misc{Nakhleh2017,
AUTHOR = {Nakhleh, Luay},
TITLE = {Phylogenetic Networks: From Displayed Trees to a Distribution of Gene Trees},
YEAR = {2017},
HOWPUBLISHED = {Phyloseminar #70},
NOTE = {https://www.youtube.com/watch?v=dkQsvLUUDcQ},
KEYWORDS = {bayesian, coalescent, explicit network, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, statistical model}
}

31

Celine Scornavacca. Occam's razor in phylogenetic network reconstruction. Phyloseminar #71, 2017.
Keywords: explicit network, from rooted trees, parsimony, phylogenetic network, phylogeny, reconstruction.
Note: https://www.youtube.com/watch?v=W6tEVulgQu8.

@Misc{Scornavacca2017,
AUTHOR = {Scornavacca, Celine},
TITLE = {Occam's razor in phylogenetic network reconstruction},
YEAR = {2017},
HOWPUBLISHED = {Phyloseminar #71},
NOTE = {https://www.youtube.com/watch?v=W6tEVulgQu8},
KEYWORDS = {explicit network, from rooted trees, parsimony, phylogenetic network, phylogeny, reconstruction}
}

32

Cécile Ané. From reconstructing to using phylogenetic networks. Phyloseminar #72, 2017.
Keywords: explicit network, from sequences, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, reconstruction, semidirected network.
Note: https://www.youtube.com/watch?v=PF4j_JOQP0c.

@Misc{Ane2017,
AUTHOR = {An{\~A}�, C{\~A}�cile},
TITLE = {From reconstructing to using phylogenetic networks},
YEAR = {2017},
HOWPUBLISHED = {Phyloseminar #72},
NOTE = {https://www.youtube.com/watch?v=PF4j_JOQP0c},
KEYWORDS = {explicit network, from sequences, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, reconstruction, semidirected network}
}

33

Paul Bastide. Shifted stochastic processes evolving on trees : application to models of adaptive evolution on phylogenies. PhD thesis, Université Paris Saclay, 2017.
Keywords: ancestral trait reconstruction, bayesian, explicit network, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, reconstruction, statistical model.
Note: https://tel.archives-ouvertes.fr/tel-01629648/en/, slides..

@PhdThesis{Bastide2017,
AUTHOR = {Bastide, Paul},
TITLE = {Shifted stochastic processes evolving on trees : application to models of adaptive evolution on phylogenies},
YEAR = {2017},
SCHOOL = {Universit{\~A}� Paris Saclay},
NOTE = {https://tel.archives-ouvertes.fr/tel-01629648/en/, slides.},
KEYWORDS = {ancestral trait reconstruction, bayesian, explicit network, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, reconstruction, statistical model}
}

34

Kuang-Yu Chang, Yun Cui, Siu-Ming Yiu and Wing-Kai Hon. Reconstructing One-Articulated Networks with Distance Matrices. In ISBRA17, Vol. 10330:34-45 of LNCS, Springer, 2017.
Keywords: explicit network, from distances, k-reticulated, phylogenetic network, phylogeny, reconstruction.
Note: https://link.springer.com/content/pdf/10.1007%2F978-3-319-59575-7.pdf#page=100.

@InProceedings{KYSW17,
AUTHOR = {Chang, Kuang-Yu and Cui, Yun and Yiu, Siu-Ming and Hon, Wing-Kai},
TITLE = {Reconstructing One-Articulated Networks with Distance Matrices},
YEAR = {2017},
BOOKTITLE = {ISBRA17},
VOLUME = {10330},
PAGES = {34-45},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {https://dx.doi.org/10.1007/978-3-319-59575-7_4},
NOTE = {https://link.springer.com/content/pdf/10.1007%2F978-3-319-59575-7.pdf#page=100},
KEYWORDS = {explicit network, from distances, k-reticulated, phylogenetic network, phylogeny, reconstruction}
}

35

Dingqiao Wen. Bayesian Inference of Phylogenetic Networks from Sequence Data. PhD thesis, Rice University, 2017.
Keywords: bayesian, explicit network, phylogenetic network, phylogeny, reconstruction.

@PhdThesis{Wen2017,
AUTHOR = {Wen, Dingqiao},
TITLE = {Bayesian Inference of Phylogenetic Networks from Sequence Data},
YEAR = {2017},
SCHOOL = {Rice University},
KEYWORDS = {bayesian, explicit network, phylogenetic network, phylogeny, reconstruction}
}

2016

1

Leo van Iersel, Steven Kelk, Nela Lekic, Chris Whidden and Norbert Zeh. Hybridization Number on Three Rooted Binary Trees is EPT. In SIDMA, Vol. 30(3):1607-1631, 2016.
Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1402.2136.

@Article{IKLWZ2016,
AUTHOR = {van Iersel, Leo and Kelk, Steven and Lekic, Nela and Whidden, Chris and Zeh, Norbert},
TITLE = {Hybridization Number on Three Rooted Binary Trees is EPT},
YEAR = {2016},
JOURNAL = {SIDMA},
VOLUME = {30},
NUMBER = {3},
PAGES = {1607-1631},
URL = {http://dx.doi.org/10.1137/15M1036579},
NOTE = {http://arxiv.org/abs/1402.2136},
KEYWORDS = {agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction}
}

2

Katharina Huber, Vincent Moulton, Mike Steel and Taoyang Wu. Folding and unfolding phylogenetic trees and networks. In JOMB, Vol. 73(6):1761-1780, 2016.
Keywords: compressed network, explicit network, FU-stable network, NP complete, phylogenetic network, phylogeny, tree containment, tree sibling network.
Note: http://arxiv.org/abs/1506.04438.

@Article{HMSW2016,
AUTHOR = {Huber, Katharina and Moulton, Vincent and Steel, Mike and Wu, Taoyang},
TITLE = {Folding and unfolding phylogenetic trees and networks},
YEAR = {2016},
JOURNAL = {JOMB},
VOLUME = {73},
NUMBER = {6},
PAGES = {1761-1780},
URL = {http://dx.doi.org/10.1007/s00285-016-0993-5},
NOTE = {http://arxiv.org/abs/1506.04438},
KEYWORDS = {compressed network, explicit network, FU-stable network, NP complete, phylogenetic network, phylogeny, tree containment, tree sibling network}
}

3

Katharina Huber, Simone Linz, Vincent Moulton and Taoyang Wu. Spaces of phylogenetic networks from generalized nearest-neighbor interchange operations. In JOMB, Vol. 72(2):699-725, 2016.
Keywords: bound, distance between networks, from network, LST distance, phylogenetic network, phylogeny.

@Article{HLMW2016,
AUTHOR = {Huber, Katharina and Linz, Simone and Moulton, Vincent and Wu, Taoyang},
TITLE = {Spaces of phylogenetic networks from generalized nearest-neighbor interchange operations},
YEAR = {2016},
JOURNAL = {JOMB},
VOLUME = {72},
NUMBER = {2},
PAGES = {699-725},
URL = {http://dx.doi.org/10.1007/s00285-015-0899-7},
KEYWORDS = {bound, distance between networks, from network, LST distance, phylogenetic network, phylogeny}
}

4

Steven Kelk, Leo van Iersel, Celine Scornavacca and Mathias Weller. Phylogenetic incongruence through the lens of Monadic Second Order logic. In JGAA, Vol. 20(2):189-215, 2016.
Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, MSOL, phylogenetic network, phylogeny, reconstruction.
Note: http://jgaa.info/accepted/2016/KelkIerselScornavaccaWeller2016.20.2.pdf.

@Article{KISW2016,
AUTHOR = {Kelk, Steven and van Iersel, Leo and Scornavacca, Celine and Weller, Mathias},
TITLE = {Phylogenetic incongruence through the lens of Monadic Second Order logic},
YEAR = {2016},
JOURNAL = {JGAA},
VOLUME = {20},
NUMBER = {2},
PAGES = {189-215},
URL = {http://dx.doi.org/10.7155/jgaa.00390},
NOTE = {http://jgaa.info/accepted/2016/KelkIerselScornavaccaWeller2016.20.2.pdf},
KEYWORDS = {agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, MSOL, phylogenetic network, phylogeny, reconstruction}
}

5

Stephen J. Willson. Comparing and simplifying distinct-cluster phylogenetic networks. In ACOM, Vol. 20(4):917-938, 2016.
Keywords: distinct-cluster network, explicit network, phylogenetic network, phylogeny.
Note: http://arxiv.org/abs/1501.07528.

@Article{Willson2016,
AUTHOR = {Willson, Stephen J.},
TITLE = {Comparing and simplifying distinct-cluster phylogenetic networks},
YEAR = {2016},
JOURNAL = {ACOM},
VOLUME = {20},
NUMBER = {4},
PAGES = {917-938},
URL = {http://dx.doi.org/10.1007/s00026-016-0324-y},
NOTE = {http://arxiv.org/abs/1501.07528},
KEYWORDS = {distinct-cluster network, explicit network, phylogenetic network, phylogeny}
}

6

Andreas Gunawan, Bhaskar DasGupta and Louxin Zhang. Locating a Tree in a Reticulation-Visible Network in Cubic Time. In RECOMB16, Vol. 9649:266 of LNBI, Springer, 2016.
Keywords: cluster containment, explicit network, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulation-visible network, tree containment.
Note: http://arxiv.org/abs/1507.02119.

@InProceedings{GDZ2016,
AUTHOR = {Gunawan, Andreas and DasGupta, Bhaskar and Zhang, Louxin},
TITLE = {Locating a Tree in a Reticulation-Visible Network in Cubic Time},
YEAR = {2016},
BOOKTITLE = {RECOMB16},
VOLUME = {9649},
PAGES = {266},
SERIES = {LNBI},
PUBLISHER = {Springer},
URL = {http://dx.doi.org/10.1007/978-3-319-31957-5},
NOTE = {http://arxiv.org/abs/1507.02119},
KEYWORDS = {cluster containment, explicit network, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulation-visible network, tree containment}
}

7

Sajad Mirzaei and Yufeng Wu. Fast Construction of Near Parsimonious Hybridization Networks for Multiple Phylogenetic Trees. In TCBB, Vol. 13(3):565-570, 2016.
Keywords: bound, explicit network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program PIRN, reconstruction, software.
Note: http://www.engr.uconn.edu/~ywu/Papers/PIRNs-preprint.pdf.

@Article{MirzaeiWu2016,
AUTHOR = {Mirzaei, Sajad and Wu, Yufeng},
TITLE = {Fast Construction of Near Parsimonious Hybridization Networks for Multiple Phylogenetic Trees},
YEAR = {2016},
JOURNAL = {TCBB},
VOLUME = {13},
NUMBER = {3},
PAGES = {565-570},
URL = {http://dx.doi.org/10.1109/TCBB.2015.2462336},
NOTE = {http://www.engr.uconn.edu/~ywu/Papers/PIRNs-preprint.pdf},
KEYWORDS = {bound, explicit network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program PIRN, reconstruction, software}
}

8

Philippe Gambette, Andreas Gunawan, Anthony Labarre, Stéphane Vialette and Louxin Zhang. Solving the Tree Containment Problem for Genetically Stable Networks in Quadratic Time. In IWOCA15, Vol. 9538:197-208 of LNCS, springer, 2016.
Keywords: explicit network, from network, from rooted trees, genetically stable network, phylogenetic network, phylogeny, polynomial, tree containment.
Note: https://hal-upec-upem.archives-ouvertes.fr/hal-01226035 .

@InProceedings{GGLVZ2016,
AUTHOR = {Gambette, Philippe and Gunawan, Andreas and Labarre, Anthony and Vialette, St{\~A}�phane and Zhang, Louxin},
TITLE = {Solving the Tree Containment Problem for Genetically Stable Networks in Quadratic Time},
YEAR = {2016},
BOOKTITLE = {IWOCA15},
VOLUME = {9538},
PAGES = {197-208},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-319-29516-9_17},
NOTE = {https://hal-upec-upem.archives-ouvertes.fr/hal-01226035 },
KEYWORDS = {explicit network, from network, from rooted trees, genetically stable network, phylogenetic network, phylogeny, polynomial, tree containment}
}

9

Magnus Bordewich and Charles Semple. Reticulation-visible networks. In Advances in Applied Mathematics, Vol. 78:114-141, 2016.
Keywords: explicit network, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, tree containment.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BS16.pdf.

@Article{BordewichSemple2016b,
AUTHOR = {Bordewich, Magnus and Semple, Charles},
TITLE = {Reticulation-visible networks},
YEAR = {2016},
JOURNAL = {Advances in Applied Mathematics},
VOLUME = {78},
PAGES = {114-141},
URL = {http://dx.doi.org/10.1016/j.aam.2016.04.004},
NOTE = {http://www.math.canterbury.ac.nz/~c.semple/papers/BS16.pdf},
KEYWORDS = {explicit network, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, tree containment}
}

10

Louxin Zhang. On Tree-Based Phylogenetic Networks. In JCB, Vol. 23(7):553-565, 2016.
Keywords: characterization, explicit network, phylogenetic network, phylogeny, tree-based network.
Note: http://arxiv.org/abs/1509.01663.

@Article{Zhang2016,
AUTHOR = {Zhang, Louxin},
TITLE = {On Tree-Based Phylogenetic Networks},
YEAR = {2016},
JOURNAL = {JCB},
VOLUME = {23},
NUMBER = {7},
PAGES = {553-565},
URL = {http://dx.doi.org/10.1089/cmb.2015.0228},
NOTE = {http://arxiv.org/abs/1509.01663},
KEYWORDS = {characterization, explicit network, phylogenetic network, phylogeny, tree-based network}
}

11

Vincent Ranwez, Celine Scornavacca, Jean-Philippe Doyon and Vincent Berry. Inferring gene duplications, transfers and losses can be done in a discrete framework. In JOMB, Vol. 72(7):1811-1844, 2016.
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction.

@Article{RSDB2016,
AUTHOR = {Ranwez, Vincent and Scornavacca, Celine and Doyon, Jean-Philippe and Berry, Vincent},
TITLE = {Inferring gene duplications, transfers and losses can be done in a discrete framework},
YEAR = {2016},
JOURNAL = {JOMB},
VOLUME = {72},
NUMBER = {7},
PAGES = {1811-1844},
URL = {http://dx.doi.org/10.1007/s00285-015-0930-z},
KEYWORDS = {duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction}
}

12

Claudia Solís-Lemus and Cécile Ané. Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting. In PLOS Genetics, Vol. 12(3):e1005896, 2016.
Keywords: explicit network, from quartets, from unrooted trees, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ.
Note: http://arxiv.org/abs/1509.06075v1.

@Article{SolisLemusAne2016,
AUTHOR = {Sol{\~A}�s-Lemus, Claudia and An{\~A}�, C{\~A}�cile},
TITLE = {Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting},
YEAR = {2016},
JOURNAL = {PLOS Genetics},
VOLUME = {12},
NUMBER = {3},
PAGES = {e1005896},
URL = {http://dx.doi.org/10.1371/journal.pgen.1005896},
NOTE = {http://arxiv.org/abs/1509.06075v1},
KEYWORDS = {explicit network, from quartets, from unrooted trees, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ}
}

13

François Chevenet, Jean-Philippe Doyon, Celine Scornavacca, Edwin Jacox, Emmanuelle Jousselin and Vincent Berry. SylvX: a viewer for phylogenetic tree reconciliations. In BIO, Vol. 32(4):608-610, 2016.
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program SylvX, software, visualization.
Note: https://www.researchgate.net/profile/Emmanuelle_Jousselin/publication/283446016_SylvX_a_viewer_for_phylogenetic_tree_reconciliations/links/5642146108aec448fa621efa.pdf.

@Article{CDSJJB2016,
AUTHOR = {Chevenet, Fran{\~A}�ois and Doyon, Jean-Philippe and Scornavacca, Celine and Jacox, Edwin and Jousselin, Emmanuelle and Berry, Vincent},
TITLE = {SylvX: a viewer for phylogenetic tree reconciliations},
YEAR = {2016},
JOURNAL = {BIO},
VOLUME = {32},
NUMBER = {4},
PAGES = {608-610},
URL = {http://dx.doi.org/10.1093/bioinformatics/btv625},
NOTE = {https://www.researchgate.net/profile/Emmanuelle_Jousselin/publication/283446016_SylvX_a_viewer_for_phylogenetic_tree_reconciliations/links/5642146108aec448fa621efa.pdf},
KEYWORDS = {duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program SylvX, software, visualization}
}

14

Jonathan Mitchell. Distinguishing Convergence on Phylogenetic Networks. PhD thesis, University of Tasmania, Australia, 2016.
Keywords: phylogenetic network, phylogeny, statistical model.
Note: http://arxiv.org/abs/1606.07160.

@PhdThesis{Mitchell2016,
AUTHOR = {Mitchell, Jonathan},
TITLE = {Distinguishing Convergence on Phylogenetic Networks},
YEAR = {2016},
SCHOOL = {University of Tasmania, Australia},
NOTE = {http://arxiv.org/abs/1606.07160},
KEYWORDS = {phylogenetic network, phylogeny, statistical model}
}

15

Rinku Mathur and Neeru Adlakha. A graph theoretic model for prediction of reticulation events and phylogenetic networks for DNA sequences. In Egyptian Journal of Basic and Applied Sciences, Vol. 3(3):263-271, 2016.
Keywords: from sequences, phylogenetic network, phylogeny, Program T REX.
Note: http://dx.doi.org/10.1016/j.ejbas.2016.07.004.

@Article{MathurAdlakha2016,
AUTHOR = {Mathur, Rinku and Adlakha, Neeru},
TITLE = {A graph theoretic model for prediction of reticulation events and phylogenetic networks for DNA sequences},
YEAR = {2016},
JOURNAL = {Egyptian Journal of Basic and Applied Sciences},
VOLUME = {3},
NUMBER = {3},
PAGES = {263-271},
URL = {http://dx.doi.org/10.1016/j.ejbas.2016.07.004},
NOTE = {http://dx.doi.org/10.1016/j.ejbas.2016.07.004},
KEYWORDS = {from sequences, phylogenetic network, phylogeny, Program T REX}
}

16

Andreas Gunawan, Bingxin Lu and Louxin Zhang. A program for verification of phylogenetic network models. In ECCB16, Vol. 32(17):i503-i510 of BIO, 2016.
Keywords: exponential algorithm, from network, from rooted trees, phylogenetic network, phylogeny, software, tree containment.
Note: http://dx.doi.org/10.1093/bioinformatics/btw467.

@InProceedings{GLZ2016,
AUTHOR = {Gunawan, Andreas and Lu, Bingxin and Zhang, Louxin},
TITLE = {A program for verification of phylogenetic network models},
YEAR = {2016},
BOOKTITLE = {ECCB16},
VOLUME = {32},
NUMBER = {17},
PAGES = {i503-i510},
SERIES = {BIO},
NOTE = {http://dx.doi.org/10.1093/bioinformatics/btw467},
KEYWORDS = {exponential algorithm, from network, from rooted trees, phylogenetic network, phylogeny, software, tree containment}
}

17

Hussein A. Hejase and Kevin J. Liu. A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation. Vol. 17(422):1-12, 2016.
Keywords: abstract network, evaluation, from sequences, phylogenetic network, phylogeny, Program PhyloNet, Program PhyloNetworks SNaQ, reconstruction, simulation, unicyclic network.
Note: http://dx.doi.org/10.1186/s12859-016-1277-1.

@Article{HejaseLiu2016,
AUTHOR = {Hejase, Hussein A. and Liu, Kevin J.},
TITLE = {A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation},
YEAR = {2016},
VOLUME = {17},
NUMBER = {422},
PAGES = {1-12},
URL = {http://dx.doi.org/10.1186/s12859-016-1277-1},
NOTE = {http://dx.doi.org/10.1186/s12859-016-1277-1},
KEYWORDS = {abstract network, evaluation, from sequences, phylogenetic network, phylogeny, Program PhyloNet, Program PhyloNetworks SNaQ, reconstruction, simulation, unicyclic network}
}

18

Ioannis G. Tollis and Konstantinos G. Kakoulis. Algorithms for Visualizing Phylogenetic Networks. In GD16, Vol. 9801:183-195 of LNCS, springer, 2016.
Keywords: explicit network, galled network, galled tree, NP complete, planar, visualization.
Note: http://arxiv.org/abs/1609.00755.

@InProceedings{TollisKakoulis2016,
AUTHOR = {Tollis, Ioannis G. and Kakoulis, Konstantinos G.},
TITLE = {Algorithms for Visualizing Phylogenetic Networks},
YEAR = {2016},
BOOKTITLE = {GD16},
VOLUME = {9801},
PAGES = {183-195},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-319-50106-2_15},
NOTE = {http://arxiv.org/abs/1609.00755},
KEYWORDS = {explicit network, galled network, galled tree, NP complete, planar, visualization}
}

19

Benjamin Albrecht. Computing Hybridization Networks Using Agreement Forests. PhD thesis, Ludwig-Maximilians-Universität München, 2016.
Note: https://edoc.ub.uni-muenchen.de/19444/.

@PhdThesis{Albrecht2016,
AUTHOR = {Albrecht, Benjamin},
TITLE = {Computing Hybridization Networks Using Agreement Forests},
YEAR = {2016},
SCHOOL = {Ludwig-Maximilians-Universit{\~A}�t M{\~A}�nchen},
NOTE = {https://edoc.ub.uni-muenchen.de/19444/}
}

20

Philippe Gambette, Leo van Iersel, Steven Kelk, Fabio Pardi and Celine Scornavacca. Do branch lengths help to locate a tree in a phylogenetic network? In BMB, Vol. 78(9):1773-1795, 2016.
Keywords: branch length, explicit network, FPT, from network, from rooted trees, NP complete, phylogenetic network, phylogeny, pseudo-polynomial, time consistent network, tree containment, tree sibling network.
Note: http://arxiv.org/abs/1607.06285.

@Article{GIKPS2016,
AUTHOR = {Gambette, Philippe and van Iersel, Leo and Kelk, Steven and Pardi, Fabio and Scornavacca, Celine},
TITLE = {Do branch lengths help to locate a tree in a phylogenetic network?},
YEAR = {2016},
JOURNAL = {BMB},
VOLUME = {78},
NUMBER = {9},
PAGES = {1773-1795},
URL = {http://dx.doi.org/10.1007/s11538-016-0199-4},
NOTE = {http://arxiv.org/abs/1607.06285},
KEYWORDS = {branch length, explicit network, FPT, from network, from rooted trees, NP complete, phylogenetic network, phylogeny, pseudo-polynomial, time consistent network, tree containment, tree sibling network}
}

21

Nikita Alexeev and Max A. Alekseyev. Combinatorial Scoring of Phylogenetic Networks. In COCOON16, Vol. 9797:560-572 of LNCS, Springer, 2016.
Keywords: cactus graph, counting, explicit network, galled tree, phylogenetic network, phylogeny.
Note: http://arxiv.org/abs/1602.02841.

@InProceedings{AlexeevAlekseyev2016,
AUTHOR = {Alexeev, Nikita and Alekseyev, Max A.},
TITLE = {Combinatorial Scoring of Phylogenetic Networks},
YEAR = {2016},
BOOKTITLE = {COCOON16},
VOLUME = {9797},
PAGES = {560-572},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {http://dx.doi.org/10.1007/978-3-319-42634-1_45},
NOTE = {http://arxiv.org/abs/1602.02841},
KEYWORDS = {cactus graph, counting, explicit network, galled tree, phylogenetic network, phylogeny}
}

22

Charles Semple. Phylogenetic Networks with Every Embedded Phylogenetic Tree a Base Tree. In BMB, Vol. 78(1):132-137, 2016.
Keywords: characterization, explicit network, phylogenetic network, phylogeny, tree-based network, tree-child network.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/S15.pdf.

@Article{Semple2016,
AUTHOR = {Semple, Charles},
TITLE = {Phylogenetic Networks with Every Embedded Phylogenetic Tree a Base Tree},
YEAR = {2016},
JOURNAL = {BMB},
VOLUME = {78},
NUMBER = {1},
PAGES = {132-137},
URL = {http://dx.doi.org/10.1007/s11538-015-0132-2},
NOTE = {http://www.math.canterbury.ac.nz/~c.semple/papers/S15.pdf},
KEYWORDS = {characterization, explicit network, phylogenetic network, phylogeny, tree-based network, tree-child network}
}

23

Katharina Huber, Vincent Moulton and Taoyang Wu. Transforming phylogenetic networks: Moving beyond tree space. In JTB, Vol. 404:30-39, 2016.
Keywords: distance between networks, level k phylogenetic network, NNI moves, phylogenetic network, phylogeny.
Note: http://arxiv.org/abs/1601.01788.

@Article{HMW2016,
AUTHOR = {Huber, Katharina and Moulton, Vincent and Wu, Taoyang},
TITLE = {Transforming phylogenetic networks: Moving beyond tree space},
YEAR = {2016},
JOURNAL = {JTB},
VOLUME = {404},
PAGES = {30-39},
URL = {http://dx.doi.org/10.1016/j.jtbi.2016.05.030},
NOTE = {http://arxiv.org/abs/1601.01788},
KEYWORDS = {distance between networks, level k phylogenetic network, NNI moves, phylogenetic network, phylogeny}
}

24

Maria Anaya, Olga Anipchenko-Ulaj, Aisha Ashfaq, Joyce Chiu, Mahedi Kaiser, Max Shoji Ohsawa, Megan Owen, Ella Pavlechko, Katherine St. John, Shivam Suleria, Keith Thompson and Corrine Yap. On Determining if Tree-based Networks Contain Fixed Trees. In BMB, Vol. 78(5):961-969, 2016.
Keywords: explicit network, FPT, NP complete, phylogenetic network, phylogeny, tree-based network.
Note: http://arxiv.org/abs/1602.02739.

@Article{AAACKOOPSSTY2016,
AUTHOR = {Anaya, Maria and Anipchenko-Ulaj, Olga and Ashfaq, Aisha and Chiu, Joyce and Kaiser, Mahedi and Ohsawa, Max Shoji and Owen, Megan and Pavlechko, Ella and St. John, Katherine and Suleria, Shivam and Thompson, Keith and Yap, Corrine},
TITLE = {On Determining if Tree-based Networks Contain Fixed Trees},
YEAR = {2016},
JOURNAL = {BMB},
VOLUME = {78},
NUMBER = {5},
PAGES = {961-969},
URL = {http://dx.doi.org/10.1007/s11538-016-0169-x},
NOTE = {http://arxiv.org/abs/1602.02739},
KEYWORDS = {explicit network, FPT, NP complete, phylogenetic network, phylogeny, tree-based network}
}

25

Momoko Hayamizu. On the existence of infinitely many universal tree-based networks. In JTB, Vol. 396:204-206, 2016.
Keywords: explicit network, phylogenetic network, phylogeny, tree-based network.
Note: http://arxiv.org/abs/1512.02402.

@Article{Hayamizu2016,
AUTHOR = {Hayamizu, Momoko},
TITLE = {On the existence of infinitely many universal tree-based networks},
YEAR = {2016},
JOURNAL = {JTB},
VOLUME = {396},
PAGES = {204-206},
URL = {http://dx.doi.org/10.1016/j.jtbi.2016.02.023},
NOTE = {http://arxiv.org/abs/1512.02402},
KEYWORDS = {explicit network, phylogenetic network, phylogeny, tree-based network}
}

26

Magnus Bordewich and Charles Semple. Determining phylogenetic networks from inter-taxa distances. In JOMB, Vol. 73(2):283-303, 2016.
Keywords: from distances, phylogenetic network, phylogeny, reconstruction, reticulation-visible network, time consistent network, tree-child network, uniqueness.
Note: http://132.181.26.35/~c.semple/papers/BS15b.pdf.

@Article{BordewichSemple2016,
AUTHOR = {Bordewich, Magnus and Semple, Charles},
TITLE = {Determining phylogenetic networks from inter-taxa distances},
YEAR = {2016},
JOURNAL = {JOMB},
VOLUME = {73},
NUMBER = {2},
PAGES = {283-303},
URL = {http://dx.doi.org/10.1007/s00285-015-0950-8},
NOTE = {http://132.181.26.35/~c.semple/papers/BS15b.pdf},
KEYWORDS = {from distances, phylogenetic network, phylogeny, reconstruction, reticulation-visible network, time consistent network, tree-child network, uniqueness}
}

27

James Oldman, Taoyang Wu, Leo van Iersel and Vincent Moulton. TriLoNet: Piecing together small networks to reconstruct reticulate evolutionary histories. In MBE, Vol. 33(8):2151-2162, 2016.
Keywords: explicit network, from subnetworks, from trinets, galled tree, phylogenetic network, phylogeny, Program LEV1ATHAN, Program TriLoNet, reconstruction.

@Article{OTIM2016,
AUTHOR = {Oldman, James and Wu, Taoyang and van Iersel, Leo and Moulton, Vincent},
TITLE = {TriLoNet: Piecing together small networks to reconstruct reticulate evolutionary histories},
YEAR = {2016},
JOURNAL = {MBE},
VOLUME = {33},
NUMBER = {8},
PAGES = {2151-2162},
URL = {http://dx.doi.org/10.1093/molbev/msw068},
KEYWORDS = {explicit network, from subnetworks, from trinets, galled tree, phylogenetic network, phylogeny, Program LEV1ATHAN, Program TriLoNet, reconstruction}
}

28

Dingqiao Wen, Yun Yu and Luay Nakhleh. Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent. In PLoS Genetics, Vol. 12(5):e1006006, 2016.
Keywords: bayesian, coalescent, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, software.

@Article{WYL2016,
AUTHOR = {Wen, Dingqiao and Yu, Yun and Nakhleh, Luay},
TITLE = {Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent},
YEAR = {2016},
JOURNAL = {PLoS Genetics},
VOLUME = {12},
NUMBER = {5},
PAGES = {e1006006},
URL = {http://dx.doi.org/10.1371/journal.pgen.1006006},
KEYWORDS = {bayesian, coalescent, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, software}
}

29

Juan Wang. A Metric on the Space of Partly Reduced Phylogenetic Networks. In BMRI, Vol. 2016(7534258):1-9, 2016.
Keywords: distance between networks, partly reduced networks, phylogenetic network, phylogeny, polynomial, reduced networks.
Note: http://downloads.hindawi.com/journals/bmri/aip/7534258.pdf.

@Article{Wang2016,
AUTHOR = {Wang, Juan},
TITLE = {A Metric on the Space of Partly Reduced Phylogenetic Networks},
YEAR = {2016},
JOURNAL = {BMRI},
VOLUME = {2016},
NUMBER = {7534258},
PAGES = {1-9},
URL = {http://dx.doi.org/10.1155/2016/7534258},
NOTE = {http://downloads.hindawi.com/journals/bmri/aip/7534258.pdf},
KEYWORDS = {distance between networks, partly reduced networks, phylogenetic network, phylogeny, polynomial, reduced networks}
}

30

Jiafan Zhu, Yun Yu and Luay Nakhleh. In the Light of Deep Coalescence: Revisiting Trees Within Networks. In RECOMB-CG16, Vol. 17(suppl. 14):415.271-282 of BMCB, 2016.
Keywords: branch length, evaluation, explicit network, incomplete lineage sorting, phylogenetic network, phylogeny, statistical model, tree-based network, weakly displaying.
Note: http://arxiv.org/abs/1606.07350.

@InProceedings{ZYN2016,
AUTHOR = {Zhu, Jiafan and Yu, Yun and Nakhleh, Luay},
TITLE = {In the Light of Deep Coalescence: Revisiting Trees Within Networks},
YEAR = {2016},
BOOKTITLE = {RECOMB-CG16},
VOLUME = {17},
NUMBER = {suppl. 14},
PAGES = {415.271-282},
SERIES = {BMCB},
URL = {http://dx.doi.org/10.1186/s12859-016-1269-1},
NOTE = {http://arxiv.org/abs/1606.07350},
KEYWORDS = {branch length, evaluation, explicit network, incomplete lineage sorting, phylogenetic network, phylogeny, statistical model, tree-based network, weakly displaying}
}

31

Magnus Bordewich and Nihan Tokac. An algorithm for reconstructing ultrametric tree-child networks from inter-taxa distances. In DAM, Vol. 213:47-59, 2016.
Keywords: explicit network, from distances, phylogenetic network, phylogeny, reconstruction, tree-child network.
Note: http://dx.doi.org/10.1016/j.dam.2016.05.011.

@Article{BordewichTokac2016,
AUTHOR = {Bordewich, Magnus and Tokac, Nihan},
TITLE = {An algorithm for reconstructing ultrametric tree-child networks from inter-taxa distances},
YEAR = {2016},
JOURNAL = {DAM},
VOLUME = {213},
PAGES = {47-59},
URL = {http://dx.doi.org/10.1016/j.dam.2016.05.011},
NOTE = {http://dx.doi.org/10.1016/j.dam.2016.05.011},
KEYWORDS = {explicit network, from distances, phylogenetic network, phylogeny, reconstruction, tree-child network}
}

32

Juan Wang, Zhang Zhibin and Yanjuan Li. Constructing phylogenetic networks based on the isomorphism of datasets. In BMRI, Vol. 2016(4236858):1-7, 2016.
Keywords: from clusters, phylogenetic network, phylogeny, reconstruction.
Note: http://downloads.hindawi.com/journals/bmri/aip/4236858.pdf.

@Article{WZL2016,
AUTHOR = {Wang, Juan and Zhibin, Zhang and Li, Yanjuan},
TITLE = {Constructing phylogenetic networks based on the isomorphism of datasets},
YEAR = {2016},
JOURNAL = {BMRI},
VOLUME = {2016},
NUMBER = {4236858},
PAGES = {1-7},
URL = {http://dx.doi.org/10.1155/2016/4236858},
NOTE = {http://downloads.hindawi.com/journals/bmri/aip/4236858.pdf},
KEYWORDS = {from clusters, phylogenetic network, phylogeny, reconstruction}
}

33

Dan Graur. Reticulate evolution and phylogenetic networks. In Molecular and Genome Evolution, Chapter 6, Sinauer, 2016.
Keywords: phylogenetic network, phylogeny, survey.
Note: http://www.sinauer.com/media/wysiwyg/samples/Graur_MGE1e_Ch06.pdf.

@InBook{Graur2016,
AUTHOR = {Graur, Dan},
TITLE = {Reticulate evolution and phylogenetic networks},
YEAR = {2016},
BOOKTITLE = {Molecular and Genome Evolution},
PUBLISHER = {Sinauer},
CHAPTER = {6},
NOTE = {http://www.sinauer.com/media/wysiwyg/samples/Graur_MGE1e_Ch06.pdf},
KEYWORDS = {phylogenetic network, phylogeny, survey}
}

34

Mike Steel. Introduction to phylogenetic networks. In Phylogeny: Discrete and Random Processes in Evolution, Vol. 89 of CBMS-NSF Regional Conference Series in Applied Mathematics, Chapter 10, SIAM, 2016.
Keywords: abstract network, explicit network, phylogenetic network, phylogeny, survey.
Note: http://bookstore.siam.org/cb89/.

@InBook{Steel2016,
AUTHOR = {Steel, Mike},
TITLE = {Introduction to phylogenetic networks},
YEAR = {2016},
BOOKTITLE = {Phylogeny: Discrete and Random Processes in Evolution},
VOLUME = {89},
SERIES = {CBMS-NSF Regional Conference Series in Applied Mathematics},
PUBLISHER = {SIAM},
CHAPTER = {10},
NOTE = {http://bookstore.siam.org/cb89/},
KEYWORDS = {abstract network, explicit network, phylogenetic network, phylogeny, survey}
}

35

Juan Wang. A Survey of Methods for Constructing Rooted Phylogenetic Networks. In PLoS ONE, Vol. 11(11):e0165834, 2016.
Keywords: evaluation, explicit network, from clusters, phylogenetic network, phylogeny, Program BIMLR, Program Dendroscope, Program LNetwork, reconstruction, survey.
Note: http://dx.doi.org/10.1371/journal.pone.0165834.

@Article{Wang2016b,
AUTHOR = {Wang, Juan},
TITLE = {A Survey of Methods for Constructing Rooted Phylogenetic Networks},
YEAR = {2016},
JOURNAL = {PLoS ONE},
VOLUME = {11},
NUMBER = {11},
PAGES = {e0165834},
URL = {http://dx.doi.org/10.1371/journal.pone.0165834},
NOTE = {http://dx.doi.org/10.1371/journal.pone.0165834},
KEYWORDS = {evaluation, explicit network, from clusters, phylogenetic network, phylogeny, Program BIMLR, Program Dendroscope, Program LNetwork, reconstruction, survey}
}

36

Nihan Tokac. Efficiency of Algorithms in Phylogenetics. PhD thesis, Durham University, U.K., 2016.
Keywords: explicit network, from distances, phylogenetic network, phylogeny, reconstruction, tree-child network.
Note: http://etheses.dur.ac.uk/11768/.

@PhdThesis{Tokac2016,
AUTHOR = {Tokac, Nihan},
TITLE = {Efficiency of Algorithms in Phylogenetics},
YEAR = {2016},
SCHOOL = {Durham University, U.K.},
URL = {http://etheses.dur.ac.uk/11768/},
NOTE = {http://etheses.dur.ac.uk/11768/},
KEYWORDS = {explicit network, from distances, phylogenetic network, phylogeny, reconstruction, tree-child network}
}

37

Leo van Iersel, Steven Kelk and Celine Scornavacca. Kernelizations for the hybridization number problem on multiple nonbinary trees. In JCSS, Vol. 82(6):1075-1089, 2016.
Keywords: explicit network, from rooted trees, kernelization, minimum number, phylogenetic network, phylogeny, Program Treeduce, reconstruction.
Note: https://arxiv.org/abs/1311.4045v3.

@Article{IKS2016,
AUTHOR = {van Iersel, Leo and Kelk, Steven and Scornavacca, Celine},
TITLE = {Kernelizations for the hybridization number problem on multiple nonbinary trees},
YEAR = {2016},
JOURNAL = {JCSS},
VOLUME = {82},
NUMBER = {6},
PAGES = {1075-1089},
URL = {https://doi.org/10.1016/j.jcss.2016.03.006},
NOTE = {https://arxiv.org/abs/1311.4045v3},
KEYWORDS = {explicit network, from rooted trees, kernelization, minimum number, phylogenetic network, phylogeny, Program Treeduce, reconstruction}
}

38

Kristina Wicke. Extending the concept of phylogenetic diversity and its measures from trees to networks. Master's thesis, Ernst-Moritz-Arndt-Universität Greifswald, 2016.
Keywords: diversity, explicit network, from network, normal network, phylogenetic network, phylogeny.
Note: https://math-inf.uni-greifswald.de/fileadmin/uni-greifswald/fakultaet/mnf/mathinf/wicke/MasterThesis_KristinaWicke.pdf.

@MastersThesis{Wicke2016,
AUTHOR = {Wicke, Kristina},
TITLE = {Extending the concept of phylogenetic diversity and its measures from trees to networks},
YEAR = {2016},
SCHOOL = {Ernst-Moritz-Arndt-Universit{\~A}�t Greifswald},
NOTE = {https://math-inf.uni-greifswald.de/fileadmin/uni-greifswald/fakultaet/mnf/mathinf/wicke/MasterThesis_KristinaWicke.pdf},
KEYWORDS = {diversity, explicit network, from network, normal network, phylogenetic network, phylogeny}
}

39

Edwin Jacox, Cédric Chauve, Gergely J. Szöllösi, Yann Ponty and Celine Scornavacca. EcceTERA: comprehensive gene tree-species tree reconciliation using parsimony. In BIO, Vol. 32(13):2056-2058, 2016.
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, parsimony, phylogenetic network, phylogeny, polynomial, Program ecceTERA.
Note: https://doi.org/10.1093/bioinformatics/btw105.

@Article{ECSPS2016,
AUTHOR = {Jacox, Edwin and Chauve, C{\~A}�dric and Sz{\~A}�ll{\~A}�si, Gergely J. and Ponty, Yann and Scornavacca, Celine},
TITLE = {EcceTERA: comprehensive gene tree-species tree reconciliation using parsimony},
YEAR = {2016},
JOURNAL = {BIO},
VOLUME = {32},
NUMBER = {13},
PAGES = {2056-2058},
URL = {https://doi.org/10.1093/bioinformatics/btw105},
NOTE = {https://doi.org/10.1093/bioinformatics/btw105},
KEYWORDS = {duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, parsimony, phylogenetic network, phylogeny, polynomial, Program ecceTERA}
}

40

Pei Wu. Quartet weights in phylogenetic network reconstruction. PhD thesis, University of Chinese Academy of Sciences, 2016.
Keywords: abstract network, from distances, from quartets, phylogenetic network, phylogeny, reconstruction, split, split network.
Note: https://www.researchgate.net/publication/324475948_Quartet_weights_in_phylogenetic_network_reconstruction.

@PhdThesis{Wu2016,
AUTHOR = {Wu, Pei},
TITLE = {Quartet weights in phylogenetic network reconstruction},
YEAR = {2016},
SCHOOL = {University of Chinese Academy of Sciences},
NOTE = {https://www.researchgate.net/publication/324475948_Quartet_weights_in_phylogenetic_network_reconstruction},
KEYWORDS = {abstract network, from distances, from quartets, phylogenetic network, phylogeny, reconstruction, split, split network}
}

41

Monika Balvociute. Flat Embeddings of Genetic and Distance Data. PhD thesis, University of Otago, 2016.
Keywords: abstract network, flat, phylogenetic network, phylogeny, planar, Program FlatNJ, Program SplitsTree, split, split network.
Note: http://hdl.handle.net/10523/6286.

@PhdThesis{Balvociute2016,
AUTHOR = {Balvociute, Monika},
TITLE = {Flat Embeddings of Genetic and Distance Data},
YEAR = {2016},
SCHOOL = {University of Otago},
URL = {http://hdl.handle.net/10523/6286},
NOTE = {http://hdl.handle.net/10523/6286},
KEYWORDS = {abstract network, flat, phylogenetic network, phylogeny, planar, Program FlatNJ, Program SplitsTree, split, split network}
}

42

Dingqiao Wen. Bayesian Inference of Phylogenetic Networks. Master's thesis, Rice University, Texas, 2016.
Keywords: bayesian, explicit network, phylogenetic network, phylogeny, Program PhyloNet, reconstruction.
Note: https://scholarship.rice.edu/bitstream/handle/1911/96515/WEN-DOCUMENT-2016.pdf?sequence=1&isAllowed=y.

@MastersThesis{Wen2016,
AUTHOR = {Wen, Dingqiao},
TITLE = {Bayesian Inference of Phylogenetic Networks},
YEAR = {2016},
SCHOOL = {Rice University, Texas},
NOTE = {https://scholarship.rice.edu/bitstream/handle/1911/96515/WEN-DOCUMENT-2016.pdf?sequence=1{\&}isAllowed=y},
KEYWORDS = {bayesian, explicit network, phylogenetic network, phylogeny, Program PhyloNet, reconstruction}
}

2015

1

Mareike Fischer, Leo van Iersel, Steven Kelk and Celine Scornavacca. On Computing The Maximum Parsimony Score Of A Phylogenetic Network. In SIDMA, Vol. 29(1):559-585, 2015.
Keywords: APX hard, cluster containment, explicit network, FPT, from network, from sequences, integer linear programming, level k phylogenetic network, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, Program MPNet, reconstruction, software.
Note: http://arxiv.org/abs/1302.2430.

@Article{FIKS2015,
AUTHOR = {Fischer, Mareike and van Iersel, Leo and Kelk, Steven and Scornavacca, Celine},
TITLE = {On Computing The Maximum Parsimony Score Of A Phylogenetic Network},
YEAR = {2015},
JOURNAL = {SIDMA},
VOLUME = {29},
NUMBER = {1},
PAGES = {559-585},
URL = {http://dx.doi.org/10.1137/140959948},
NOTE = {http://arxiv.org/abs/1302.2430},
KEYWORDS = {APX hard, cluster containment, explicit network, FPT, from network, from sequences, integer linear programming, level k phylogenetic network, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, Program MPNet, reconstruction, software}
}

2

Colin McDiarmid, Charles Semple and Dominic Welsh. Counting phylogenetic networks. In Annals of Combinatorics, Vol. 19(1):205-224, 2015.
Keywords: counting, explicit network, normal network, phylogenetic network, phylogeny, tree-child network.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/MSW13.pdf.

@Article{MSW2015,
AUTHOR = {McDiarmid, Colin and Semple, Charles and Welsh, Dominic},
TITLE = {Counting phylogenetic networks},
YEAR = {2015},
JOURNAL = {Annals of Combinatorics},
VOLUME = {19},
NUMBER = {1},
PAGES = {205-224},
URL = {http://dx.doi.org/10.1007/s00026-015-0260-2},
NOTE = {http://www.math.canterbury.ac.nz/~c.semple/papers/MSW13.pdf},
KEYWORDS = {counting, explicit network, normal network, phylogenetic network, phylogeny, tree-child network}
}

3

Andrew R. Francis and Mike Steel. Tree-like Reticulation Networks - When Do Tree-like Distances Also Support Reticulate Evolution? In MBIO, Vol. 259:12-19, 2015.
Keywords: from distances, phylogenetic network, phylogeny.
Note: http://arxiv.org/abs/1405.2965.

@Article{FrancisSteel2015a,
AUTHOR = {Francis, Andrew R. and Steel, Mike},
TITLE = {Tree-like Reticulation Networks - When Do Tree-like Distances Also Support Reticulate Evolution?},
YEAR = {2015},
JOURNAL = {MBIO},
VOLUME = {259},
PAGES = {12-19},
URL = {http://dx.doi.org/10.1016/j.mbs.2014.10.008},
NOTE = {http://arxiv.org/abs/1405.2965},
KEYWORDS = {from distances, phylogenetic network, phylogeny}
}

4

Katharina Huber, Leo van Iersel, Vincent Moulton and Taoyang Wu. How much information is needed to infer reticulate evolutionary histories? In Systematic Biology, Vol. 64(1):102-111, 2015.
Keywords: explicit network, from network, from rooted trees, from subnetworks, from trinets, identifiability, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: http://dx.doi.org/10.1093/sysbio/syu076.

@Article{HIMW2015,
AUTHOR = {Huber, Katharina and van Iersel, Leo and Moulton, Vincent and Wu, Taoyang},
TITLE = {How much information is needed to infer reticulate evolutionary histories?},
YEAR = {2015},
JOURNAL = {Systematic Biology},
VOLUME = {64},
NUMBER = {1},
PAGES = {102-111},
URL = {http://dx.doi.org/10.1093/sysbio/syu076},
NOTE = {http://dx.doi.org/10.1093/sysbio/syu076},
KEYWORDS = {explicit network, from network, from rooted trees, from subnetworks, from trinets, identifiability, phylogenetic network, phylogeny, reconstruction, uniqueness}
}

5

Andrew R. Francis and Mike Steel. Which phylogenetic networks are merely trees with additional arcs? In Systematic Biology, Vol. 64(5):768-777, 2015.
Keywords: explicit network, phylogenetic network, phylogeny, polynomial, tree-based network.
Note: http://arxiv.org/abs/1502.07045.

@Article{FrancisSteel2015,
AUTHOR = {Francis, Andrew R. and Steel, Mike},
TITLE = {Which phylogenetic networks are merely trees with additional arcs?},
YEAR = {2015},
JOURNAL = {Systematic Biology},
VOLUME = {64},
NUMBER = {5},
PAGES = {768-777},
URL = {http://dx.doi.org/10.1093/sysbio/syv037},
NOTE = {http://arxiv.org/abs/1502.07045},
KEYWORDS = {explicit network, phylogenetic network, phylogeny, polynomial, tree-based network}
}

6

Fabio Pardi and Celine Scornavacca. Reconstructible Phylogenetic Networks: Do Not Distinguish the Indistinguishable. In PLoS Computational Biology, Vol. 11(4):e1007137.1-23, 2015.
Keywords: branch length, explicit network, from rooted trees, identifiability, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1371/journal.pcbi.1004135.

@Article{PardiScornavacca2015,
AUTHOR = {Pardi, Fabio and Scornavacca, Celine},
TITLE = {Reconstructible Phylogenetic Networks: Do Not Distinguish the Indistinguishable},
YEAR = {2015},
JOURNAL = {PLoS Computational Biology},
VOLUME = {11},
NUMBER = {4},
PAGES = {e1007137.1-23},
URL = {http://dx.doi.org/10.1371/journal.pcbi.1004135},
NOTE = {http://dx.doi.org/10.1371/journal.pcbi.1004135},
KEYWORDS = {branch length, explicit network, from rooted trees, identifiability, phylogenetic network, phylogeny, reconstruction}
}

7

Philippe Gambette, Andreas Gunawan, Anthony Labarre, Stéphane Vialette and Louxin Zhang. Locating a Tree in A Phylogenetic Network in Quadratic Time. In RECOMB15, Vol. 9029:96-107 of LNCS, Springer, 2015.
Keywords: evaluation, explicit network, from network, from rooted trees, genetically stable network, nearly-stable network, phylogenetic network, phylogeny, polynomial, tree containment.
Note: https://hal.archives-ouvertes.fr/hal-01116231/en.

@InProceedings{GGLVZ2015,
AUTHOR = {Gambette, Philippe and Gunawan, Andreas and Labarre, Anthony and Vialette, St{\~A}�phane and Zhang, Louxin},
TITLE = {Locating a Tree in A Phylogenetic Network in Quadratic Time},
YEAR = {2015},
BOOKTITLE = {RECOMB15},
VOLUME = {9029},
PAGES = {96-107},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {http://dx.doi.org/10.1007/978-3-319-16706-0_12},
NOTE = {https://hal.archives-ouvertes.fr/hal-01116231/en},
KEYWORDS = {evaluation, explicit network, from network, from rooted trees, genetically stable network, nearly-stable network, phylogenetic network, phylogeny, polynomial, tree containment}
}

8

Dan Gusfield. Persistent Phylogeny: A Galled-Tree and Integer Linear Programming Approach. In BCB15, Pages 443-451, 2015.
Keywords: explicit network, from binary characters, galled tree, integer linear programming, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1506.00678.

@InProceedings{Gusfield2015,
AUTHOR = {Gusfield, Dan},
TITLE = {Persistent Phylogeny: A Galled-Tree and Integer Linear Programming Approach},
YEAR = {2015},
BOOKTITLE = {BCB15},
PAGES = {443-451},
URL = {http://dx.doi.org/10.1145/2808719.2808765},
NOTE = {http://arxiv.org/abs/1506.00678},
KEYWORDS = {explicit network, from binary characters, galled tree, integer linear programming, phylogenetic network, phylogeny, reconstruction}
}

9

Quan Nguyen. Likelihood-based Phylogenetic Network Inference by Approximate Structural Expectation Maximization. Master's thesis, University of Helsinki, 2015.
Keywords: BIC, likelihood, phylogenetic network, phylogeny, Program PhyloDAG, reconstruction, software.
Note: http://urn.fi/URN:NBN:fi-fe2015062910525.

@MastersThesis{Nguyen2015,
AUTHOR = {Nguyen, Quan},
TITLE = {Likelihood-based Phylogenetic Network Inference by Approximate Structural Expectation Maximization},
YEAR = {2015},
SCHOOL = {University of Helsinki},
URL = {http://urn.fi/URN:NBN:fi-fe2015062910525},
NOTE = {http://urn.fi/URN:NBN:fi-fe2015062910525},
KEYWORDS = {BIC, likelihood, phylogenetic network, phylogeny, Program PhyloDAG, reconstruction, software}
}

10

Quan Nguyen and Teemu Roos. Likelihood-based inference of phylogenetic networks from sequence data by PhyloDAG. In AlCoB15, Vol. 9199:126-140 of LNCS, springer, 2015.
Keywords: BIC, explicit network, from sequences, likelihood, phylogenetic network, phylogeny, Program PhyloDAG, reconstruction, software.
Note: http://www.cs.helsinki.fi/u/ttonteri/pub/alcob2015.pdf.

@InProceedings{NguyenRoos2015,
AUTHOR = {Nguyen, Quan and Roos, Teemu},
TITLE = {Likelihood-based inference of phylogenetic networks from sequence data by PhyloDAG},
YEAR = {2015},
BOOKTITLE = {AlCoB15},
VOLUME = {9199},
PAGES = {126-140},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-319-21233-3_10},
NOTE = {http://www.cs.helsinki.fi/u/ttonteri/pub/alcob2015.pdf},
KEYWORDS = {BIC, explicit network, from sequences, likelihood, phylogenetic network, phylogeny, Program PhyloDAG, reconstruction, software}
}

11

Vladimir Ulyantsev and Mikhail Melnik. Constructing Parsimonious Hybridization Networks from Multiple Phylogenetic Trees Using a SAT-solver. In AlCoB15, Vol. 9199:141-153 of LNCS, springer, 2015.
Keywords: explicit network, from rooted trees, from trees, phylogenetic network, phylogeny, Program PIRN, reconstruction.
Note: https://www.researchgate.net/profile/Vladimir_Ulyantsev/publication/282816862_Constructing_Parsimonious_Hybridization_Networks_from_Multiple_Phylogenetic_Trees_Using_a_SAT-Solver/links/561d372c08aecade1acb3699/Constructing-Parsimonious-Hybridization-Networks-from-Multiple-Phylogenetic-Trees-Using-a-SAT-Solver.pdf.

@InProceedings{UlyantsevMelnik2015,
AUTHOR = {Ulyantsev, Vladimir and Melnik, Mikhail},
TITLE = {Constructing Parsimonious Hybridization Networks from Multiple Phylogenetic Trees Using a SAT-solver},
YEAR = {2015},
BOOKTITLE = {AlCoB15},
VOLUME = {9199},
PAGES = {141-153},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-319-21233-3_11},
NOTE = {https://www.researchgate.net/profile/Vladimir_Ulyantsev/publication/282816862_Constructing_Parsimonious_Hybridization_Networks_from_Multiple_Phylogenetic_Trees_Using_a_SAT-Solver/links/561d372c08aecade1acb3699/Constructing-Parsimonious-Hybridization-Networks-from-Multiple-Phylogenetic-Trees-Using-a-SAT-Solver.pdf},
KEYWORDS = {explicit network, from rooted trees, from trees, phylogenetic network, phylogeny, Program PIRN, reconstruction}
}

12

Jittat Fakcharoenphol, Tanee Kumpijit and Attakorn Putwattana. A Faster Algorithm for the Tree Containment Problem for Binary Nearly Stable Phylogenetic Networks. In Proceedings of the The 12th International Joint Conference on Computer Science and Software Engineering (JCSSE'15), Pages 337-342, IEEE, 2015.
Keywords: dynamic programming, explicit network, from network, from rooted trees, nearly-stable network, phylogenetic network, phylogeny, polynomial, tree containment.

@InProceedings{FKP2015,
AUTHOR = {Fakcharoenphol, Jittat and Kumpijit, Tanee and Putwattana, Attakorn},
TITLE = {A Faster Algorithm for the Tree Containment Problem for Binary Nearly Stable Phylogenetic Networks},
YEAR = {2015},
BOOKTITLE = {Proceedings of the The 12th International Joint Conference on Computer Science and Software Engineering (JCSSE'15)},
PAGES = {337-342},
PUBLISHER = {IEEE},
URL = {http://dx.doi.org/10.1109/JCSSE.2015.7219820},
KEYWORDS = {dynamic programming, explicit network, from network, from rooted trees, nearly-stable network, phylogenetic network, phylogeny, polynomial, tree containment}
}

13

Misagh Kordi and Mukul S. Bansal. On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees. In ISBRA15, Vol. 9096:187-198 of LNCS, springer, 2015.
Keywords: duplication, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: http://compbio.engr.uconn.edu/papers/Kordi_ISBRA2015.pdf.

@InProceedings{KordiBansal2015,
AUTHOR = {Kordi, Misagh and Bansal, Mukul S.},
TITLE = {On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees},
YEAR = {2015},
BOOKTITLE = {ISBRA15},
VOLUME = {9096},
PAGES = {187-198},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-319-19048-8_16},
NOTE = {http://compbio.engr.uconn.edu/papers/Kordi_ISBRA2015.pdf},
KEYWORDS = {duplication, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction}
}

14

Yun Yu and Luay Nakhleh. A Distance-Based Method for Inferring Phylogenetic Networks in the Presence of Incomplete Lineage Sorting. In ISBRA15, Vol. 9096:378-389 of LNCS, springer, 2015.
Keywords: bootstrap, explicit network, from distances, heuristic, incomplete lineage sorting, phylogenetic network, phylogeny, reconstruction.
Note: http://bioinfo.cs.rice.edu/sites/bioinfo.cs.rice.edu/files/YuNakhleh-ISBRA15.pdf.

@InProceedings{YuNakhleh2015,
AUTHOR = {Yu, Yun and Nakhleh, Luay},
TITLE = {A Distance-Based Method for Inferring Phylogenetic Networks in the Presence of Incomplete Lineage Sorting},
YEAR = {2015},
BOOKTITLE = {ISBRA15},
VOLUME = {9096},
PAGES = {378-389},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-319-19048-8_32},
NOTE = {http://bioinfo.cs.rice.edu/sites/bioinfo.cs.rice.edu/files/YuNakhleh-ISBRA15.pdf},
KEYWORDS = {bootstrap, explicit network, from distances, heuristic, incomplete lineage sorting, phylogenetic network, phylogeny, reconstruction}
}

15

Benjamin Albrecht. Computing all hybridization networks for multiple binary phylogenetic input trees. In BMCB, Vol. 16(236):1-15, 2015.
Keywords: agreement forest, explicit network, exponential algorithm, FPT, from rooted trees, phylogenetic network, phylogeny, Program Hybroscale, Program PIRN, reconstruction.
Note: http://dx.doi.org/10.1186/s12859-015-0660-7.

@Article{Albrecht2015,
AUTHOR = {Albrecht, Benjamin},
TITLE = {Computing all hybridization networks for multiple binary phylogenetic input trees},
YEAR = {2015},
JOURNAL = {BMCB},
VOLUME = {16},
NUMBER = {236},
PAGES = {1-15},
URL = {http://dx.doi.org/10.1186/s12859-015-0660-7},
NOTE = {http://dx.doi.org/10.1186/s12859-015-0660-7},
KEYWORDS = {agreement forest, explicit network, exponential algorithm, FPT, from rooted trees, phylogenetic network, phylogeny, Program Hybroscale, Program PIRN, reconstruction}
}

16

Johannes Fischer and Daniel Peters. A Practical Succinct Data Structure for Tree-Like Graphs. In WALCOM15, Vol. 8973:65-76 of LNCS, springer, 2015.
Keywords: compression, from network, phylogenetic network, phylogeny.

@InProceedings{FischerPeters2015,
AUTHOR = {Fischer, Johannes and Peters, Daniel},
TITLE = {A Practical Succinct Data Structure for Tree-Like Graphs},
YEAR = {2015},
BOOKTITLE = {WALCOM15},
VOLUME = {8973},
PAGES = {65-76},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-319-15612-5_7},
KEYWORDS = {compression, from network, phylogenetic network, phylogeny}
}

17

Ward C Wheeler. Phylogenetic network analysis as a parsimony optimization problem. In BMCB, Vol. 16(296):1-9, 2015.
Keywords: explicit network, from sequences, parsimony, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1186/s12859-015-0675-0.

@Article{Wheeler2015,
AUTHOR = {Wheeler, Ward C},
TITLE = {Phylogenetic network analysis as a parsimony optimization problem},
YEAR = {2015},
JOURNAL = {BMCB},
VOLUME = {16},
NUMBER = {296},
PAGES = {1-9},
URL = {http://dx.doi.org/10.1186/s12859-015-0675-0},
NOTE = {http://dx.doi.org/10.1186/s12859-015-0675-0},
KEYWORDS = {explicit network, from sequences, parsimony, phylogenetic network, phylogeny, reconstruction}
}

18

Maxime Morgado. Propriétés structurelles et relations des classes de réseaux phylogénétiques. Master's thesis, ENS Cachan, 2015.
Keywords: compressed network, distinct-cluster network, explicit network, galled network, galled tree, level k phylogenetic network, nested network, normal network, phylogenetic network, phylogeny, regular network, spread, tree containment, tree sibling network, tree-based network, tree-child network, unicyclic network.

@MastersThesis{Morgado2015,
AUTHOR = {Morgado, Maxime},
TITLE = {Propri{\~A}�t{\~A}�s structurelles et relations des classes de r{\~A}�seaux phylog{\~A}�n{\~A}�tiques},
YEAR = {2015},
SCHOOL = {ENS Cachan},
KEYWORDS = {compressed network, distinct-cluster network, explicit network, galled network, galled tree, level k phylogenetic network, nested network, normal network, phylogenetic network, phylogeny, regular network, spread, tree containment, tree sibling network, tree-based network, tree-child network, unicyclic network}
}

19

Yun Yu and Luay Nakhleh. A maximum pseudo-likelihood approach for phylogenetic networks. In RECOMB-CG15, Vol. 16(Suppl 10)(S10):1-10 of BMC Genomics, BioMed Central, 2015.
Keywords: explicit network, from rooted trees, hybridization, incomplete lineage sorting, likelihood, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, tripartition distance.
Note: http://dx.doi.org/10.1186/1471-2164-16-S10-S10.

@InProceedings{YuNakhleh2015b,
AUTHOR = {Yu, Yun and Nakhleh, Luay},
TITLE = {A maximum pseudo-likelihood approach for phylogenetic networks},
YEAR = {2015},
BOOKTITLE = {RECOMB-CG15},
VOLUME = {16(Suppl 10)},
NUMBER = {S10},
PAGES = {1-10},
SERIES = {BMC Genomics},
PUBLISHER = {BioMed Central},
URL = {http://dx.doi.org/10.1186/1471-2164-16-S10-S10},
NOTE = {http://dx.doi.org/10.1186/1471-2164-16-S10-S10},
KEYWORDS = {explicit network, from rooted trees, hybridization, incomplete lineage sorting, likelihood, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, tripartition distance}
}

20

Sha Zhu, James H. Degnan, Sharyn J. Goldstein and Bjarki Eldon. Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees. In BMCB, Vol. 16(292):1-7, 2015.
Keywords: explicit network, from network, phylogenetic network, phylogeny, Program Hybrid-Lambda, simulation, software.
Note: http://dx.doi.org/10.1186/s12859-015-0721-y.

@Article{ZDGE2015,
AUTHOR = {Zhu, Sha and Degnan, James H. and Goldstein, Sharyn J. and Eldon, Bjarki},
TITLE = {Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees},
YEAR = {2015},
JOURNAL = {BMCB},
VOLUME = {16},
NUMBER = {292},
PAGES = {1-7},
URL = {http://dx.doi.org/10.1186/s12859-015-0721-y},
NOTE = {http://dx.doi.org/10.1186/s12859-015-0721-y},
KEYWORDS = {explicit network, from network, phylogenetic network, phylogeny, Program Hybrid-Lambda, simulation, software}
}

21

Gergely J. Szöllösi, Adrián Arellano Davín, Eric Tannier, Vincent Daubin and Bastien Boussau. Genome-scale phylogenetic analysis finds extensive gene transfer among fungi. In Philosophical Transactions of the Royal Society of London B: Biological Sciences, Vol. 370(1678):1-11, 2015.
Keywords: duplication, from sequences, lateral gene transfer, loss, phylogenetic network, phylogeny, Program ALE, reconstruction.
Note: http://dx.doi.org/10.1098/rstb.2014.0335.

@Article{SDTDB2015,
AUTHOR = {Sz{\~A}�ll{\~A}�si, Gergely J. and Dav{\~A}�n, Adri{\~A}�n Arellano and Tannier, Eric and Daubin, Vincent and Boussau, Bastien},
TITLE = {Genome-scale phylogenetic analysis finds extensive gene transfer among fungi},
YEAR = {2015},
JOURNAL = {Philosophical Transactions of the Royal Society of London B: Biological Sciences},
VOLUME = {370},
NUMBER = {1678},
PAGES = {1-11},
URL = {http://dx.doi.org/10.1098/rstb.2014.0335},
NOTE = {http://dx.doi.org/10.1098/rstb.2014.0335},
KEYWORDS = {duplication, from sequences, lateral gene transfer, loss, phylogenetic network, phylogeny, Program ALE, reconstruction}
}

22

Thu-Hien To and Celine Scornavacca. Efficient algorithms for reconciling gene trees and species networks via duplication and loss events. In RECOMB-CG15, Vol. 16(Suppl 10)(S6):1-14 of BMC Genomics, BioMed Central, 2015.
Keywords: explicit network, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://dx.doi.org/10.1186/1471-2164-16-S10-S6.

@InProceedings{ToScornavacca2015,
AUTHOR = {To, Thu-Hien and Scornavacca, Celine},
TITLE = {Efficient algorithms for reconciling gene trees and species networks via duplication and loss events},
YEAR = {2015},
BOOKTITLE = {RECOMB-CG15},
VOLUME = {16(Suppl 10)},
NUMBER = {S6},
PAGES = {1-14},
SERIES = {BMC Genomics},
PUBLISHER = {BioMed Central},
URL = {http://dx.doi.org/10.1186/1471-2164-16-S10-S6},
NOTE = {http://dx.doi.org/10.1186/1471-2164-16-S10-S6},
KEYWORDS = {explicit network, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reconstruction}
}

23

Dwueng-Chwuan Jhwueng and Brian O'Meara. Trait Evolution on Phylogenetic Networks. 2015.
Keywords: explicit network, from network, hybridization, phylogenetic network, phylogeny, Program BMhyd, statistical model.
Note: http://dx.doi.org/10.1101/023986.

@Misc{JhwuengOMeara2015,
AUTHOR = {Jhwueng, Dwueng-Chwuan and O'Meara, Brian},
TITLE = {Trait Evolution on Phylogenetic Networks},
YEAR = {2015},
URL = {http://dx.doi.org/10.1101/023986},
NOTE = {http://dx.doi.org/10.1101/023986},
KEYWORDS = {explicit network, from network, hybridization, phylogenetic network, phylogeny, Program BMhyd, statistical model}
}

24

Andreas Gunawan and Louxin Zhang. Bounding the Size of a Network Defined By Visibility Property. 2015.
Keywords: bound, explicit network, galled network, nearly-stable network, phylogenetic network, phylogeny, reticulation-visible network, stable-child network.
Note: http://arxiv.org/abs/1510.00115.

@Misc{GunawanZhang2015,
AUTHOR = {Gunawan, Andreas and Zhang, Louxin},
TITLE = {Bounding the Size of a Network Defined By Visibility Property},
YEAR = {2015},
NOTE = {http://arxiv.org/abs/1510.00115},
KEYWORDS = {bound, explicit network, galled network, nearly-stable network, phylogenetic network, phylogeny, reticulation-visible network, stable-child network}
}

25

Marc Thuillard and Didier Fraix-Burnet. Phylogenetic Trees and Networks Reduce to Phylogenies on Binary States: Does It Furnish an Explanation to the Robustness of Phylogenetic Trees against Lateral Transfers? In Evolutionary Bioinformatics, Vol. 11:213-221, 2015. [Abstract]
Keywords: circular split system, explicit network, from multistate characters, outerplanar, perfect, phylogenetic network, phylogeny, planar, polynomial, reconstruction, split.
Note: http://dx.doi.org/10.4137%2FEBO.S28158.

@Article{ThuillardFraixBurnet2015,
AUTHOR = {Thuillard, Marc and Fraix-Burnet, Didier},
TITLE = {Phylogenetic Trees and Networks Reduce to Phylogenies on Binary States: Does It Furnish an Explanation to the Robustness of Phylogenetic Trees against Lateral Transfers?},
YEAR = {2015},
JOURNAL = {Evolutionary Bioinformatics},
VOLUME = {11},
PAGES = {213-221},
URL = {http://dx.doi.org/10.4137/EBO.S28158},
ABSTRACT = {This article presents an innovative approach to phylogenies based on the reduction of multistate characters to binary-state characters. We show that the reduction to binary characters{\^a}�� approach can be applied to both character- and distance-based phylogenies and provides a unifying framework to explain simply and intuitively the similarities and differences between distance- and character-based phylogenies. Building on these results, this article gives a possible explanation on why phylogenetic trees obtained from a distance matrix or a set of characters are often quite reasonable despite lateral transfers of genetic material between taxa. In the presence of lateral transfers, outer planar networks furnish a better description of evolution than phylogenetic trees. We present a polynomial-time reconstruction algorithm for perfect outer planar networks with a fixed number of states, characters, and lateral transfers.},
NOTE = {http://dx.doi.org/10.4137%2FEBO.S28158},
KEYWORDS = {circular split system, explicit network, from multistate characters, outerplanar, perfect, phylogenetic network, phylogeny, planar, polynomial, reconstruction, split}
}

26

Laura Jetten. Characterising tree-based phylogenetic networks. Bachelor thesis, 2015.
Keywords: characterization, explicit network, phylogenetic network, phylogeny, tree-based network.
Note: http://resolver.tudelft.nl/uuid:fda2636d-0ed5-4dd2-bacf-8abbbad8994e.

@Misc{Jetten2015,
AUTHOR = {Jetten, Laura},
TITLE = {Characterising tree-based phylogenetic networks},
YEAR = {2015},
HOWPUBLISHED = {Bachelor thesis},
NOTE = {http://resolver.tudelft.nl/uuid:fda2636d-0ed5-4dd2-bacf-8abbbad8994e},
KEYWORDS = {characterization, explicit network, phylogenetic network, phylogeny, tree-based network}
}

27

Benjamin Albrecht. Computing a Relevant Set of Nonbinary Maximum Acyclic Agreement Forests. 2015.
Keywords: agreement forest, explicit network, exponential algorithm, from rooted trees, phylogenetic network, phylogeny, Program Hybroscale, reconstruction, software.
Note: http://arxiv.org/abs/1512.05703.

@Misc{Albrecht2015a,
AUTHOR = {Albrecht, Benjamin},
TITLE = {Computing a Relevant Set of Nonbinary Maximum Acyclic Agreement Forests},
YEAR = {2015},
NOTE = {http://arxiv.org/abs/1512.05703},
KEYWORDS = {agreement forest, explicit network, exponential algorithm, from rooted trees, phylogenetic network, phylogeny, Program Hybroscale, reconstruction, software}
}

28

Benjamin Albrecht. Fast computation of all maximum acyclic agreement forests for two rooted binary phylogenetic trees. 2015.
Keywords: agreement forest, explicit network, from rooted trees, phylogenetic network, phylogeny, Program Hybroscale, reconstruction, software.
Note: http://arxiv.org/abs/1512.05656.

@Misc{Albrecht2015b,
AUTHOR = {Albrecht, Benjamin},
TITLE = {Fast computation of all maximum acyclic agreement forests for two rooted binary phylogenetic trees},
YEAR = {2015},
NOTE = {http://arxiv.org/abs/1512.05656},
KEYWORDS = {agreement forest, explicit network, from rooted trees, phylogenetic network, phylogeny, Program Hybroscale, reconstruction, software}
}

29

Nela Lekic. Trees, agreement forests and treewidth: combinatorial algorithms for constructing phylogenetic networks. PhD thesis, Maastricht University, The Netherlands, 2015.
Keywords: explicit network, from rooted trees, phylogenetic network, phylogeny, reconstruction.

@PhdThesis{Lekic2015,
AUTHOR = {Lekic, Nela},
TITLE = {Trees, agreement forests and treewidth: combinatorial algorithms for constructing phylogenetic networks},
YEAR = {2015},
SCHOOL = {Maastricht University, The Netherlands},
KEYWORDS = {explicit network, from rooted trees, phylogenetic network, phylogeny, reconstruction}
}

30

Jessica W. Leigh and David Bryant. PopART: full-feature software for haplotype network construction. In Methods in Ecology and Evolution, Vol. 6(9):1110-1116, 2015.
Keywords: abstract network, from sequences, haplotype network, MedianJoining, phylogenetic network, phylogeny, population genetics, Program PopART, Program TCS, software.
Note: http://dx.doi.org/10.1111/2041-210X.12410.

@Article{LeighBryant2015,
AUTHOR = {Leigh, Jessica W. and Bryant, David},
TITLE = {PopART: full-feature software for haplotype network construction},
YEAR = {2015},
JOURNAL = {Methods in Ecology and Evolution},
VOLUME = {6},
NUMBER = {9},
PAGES = {1110-1116},
URL = {http://dx.doi.org/10.1111/2041-210X.12410},
NOTE = {http://dx.doi.org/10.1111/2041-210X.12410},
KEYWORDS = {abstract network, from sequences, haplotype network, MedianJoining, phylogenetic network, phylogeny, population genetics, Program PopART, Program TCS, software}
}

31

Gabriel Cardona, Joan Carles Pons and Francesc Rosselló. A reconstruction problem for a class of phylogenetic networks with lateral gene transfers. In ALMOB, Vol. 10(28):1-15, 2015.
Keywords: explicit network, from rooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program LGTnetwork, reconstruction, software, tree-based network.
Note: http://dx.doi.org/10.1186/s13015-015-0059-z.

@Article{CPR2015,
AUTHOR = {Cardona, Gabriel and Pons, Joan Carles and Rossell{\~A}�, Francesc},
TITLE = {A reconstruction problem for a class of phylogenetic networks with lateral gene transfers},
YEAR = {2015},
JOURNAL = {ALMOB},
VOLUME = {10},
NUMBER = {28},
PAGES = {1-15},
URL = {http://dx.doi.org/10.1186/s13015-015-0059-z},
NOTE = {http://dx.doi.org/10.1186/s13015-015-0059-z},
KEYWORDS = {explicit network, from rooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program LGTnetwork, reconstruction, software, tree-based network}
}

32

Claudia Solís-Lemus. Statistical methods to infer population structure with coalescence and gene flow. PhD thesis, University of Wisconsin-Madison, 2015.
Keywords: explicit network, from quartets, from unrooted trees, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, semidirected network.
Note: https://www.stat.wisc.edu/~claudia/thesis.pdf.

@PhdThesis{SolisLemus2015,
AUTHOR = {Sol{\~A}�s-Lemus, Claudia},
TITLE = {Statistical methods to infer population structure with coalescence and gene flow},
YEAR = {2015},
SCHOOL = {University of Wisconsin-Madison},
NOTE = {https://www.stat.wisc.edu/~claudia/thesis.pdf},
KEYWORDS = {explicit network, from quartets, from unrooted trees, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, semidirected network}
}

2014

1

Leo van Iersel, Steven Kelk, Nela Lekic and Leen Stougie. Approximation algorithms for nonbinary agreement forests. In SIDMA, Vol. 28(1):49-66, 2014.
Keywords: agreement forest, approximation, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1210.3211.

Toggle abstract

@Article{IKLS2014,
AUTHOR = {van Iersel, Leo and Kelk, Steven and Lekic, Nela and Stougie, Leen},
TITLE = {Approximation algorithms for nonbinary agreement forests},
YEAR = {2014},
JOURNAL = {SIDMA},
VOLUME = {28},
NUMBER = {1},
PAGES = {49-66},
URL = {http://dx.doi.org/10.1137/120903567},
NOTE = {http://arxiv.org/abs/1210.3211},
KEYWORDS = {agreement forest, approximation, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction}
}

2

Gabriel Cardona, Mercè Llabrés, Francesc Rosselló and Gabriel Valiente. The comparison of tree-sibling time consistent phylogenetic networks is graph-isomorphism complete. In The Scientific World Journal, Vol. 2014(254279):1-6, 2014.
Keywords: abstract network, distance between networks, from network, isomorphism, phylogenetic network, tree sibling network.
Note: http://arxiv.org/abs/0902.4640.

Toggle abstract

@Article{CLRV2014,
AUTHOR = {Cardona, Gabriel and Llabr{\~A}�s, Merc{\~A}� and Rossell{\~A}�, Francesc and Valiente, Gabriel},
TITLE = {The comparison of tree-sibling time consistent phylogenetic networks is graph-isomorphism complete},
YEAR = {2014},
JOURNAL = {The Scientific World Journal},
VOLUME = {2014},
NUMBER = {254279},
PAGES = {1-6},
URL = {http://dx.doi.org/10.1155/2014/254279},
NOTE = {http://arxiv.org/abs/0902.4640},
KEYWORDS = {abstract network, distance between networks, from network, isomorphism, phylogenetic network, tree sibling network}
}

3

Steven Kelk and Celine Scornavacca. Constructing minimal phylogenetic networks from softwired clusters is fixed parameter tractable. In ALG, Vol. 68(4):886-915, 2014.
Keywords: explicit network, FPT, from clusters, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1108.3653.

Toggle abstract

@Article{KelkScornavacca2014,
AUTHOR = {Kelk, Steven and Scornavacca, Celine},
TITLE = {Constructing minimal phylogenetic networks from softwired clusters is fixed parameter tractable},
YEAR = {2014},
JOURNAL = {ALG},
VOLUME = {68},
NUMBER = {4},
PAGES = {886-915},
URL = {http://dx.doi.org/10.1007/s00453-012-9708-5},
NOTE = {http://arxiv.org/abs/1108.3653},
KEYWORDS = {explicit network, FPT, from clusters, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction}
}

4

Hadi Poormohammadi, Changiz Eslahchi and Ruzbeh Tusserkani. TripNet: A Method for Constructing Rooted Phylogenetic Networks from Rooted Triplets. In PLoS ONE, Vol. 9(9):e106531, 2014.
Keywords: explicit network, from triplets, heuristic, level k phylogenetic network, phylogenetic network, phylogeny, Program TripNet, reconstruction, software.
Note: http://arxiv.org/abs/1201.3722.

Toggle abstract

@Article{HCR2014,
AUTHOR = {Poormohammadi, Hadi and Eslahchi, Changiz and Tusserkani, Ruzbeh},
TITLE = {TripNet: A Method for Constructing Rooted Phylogenetic Networks from Rooted Triplets},
YEAR = {2014},
JOURNAL = {PLoS ONE},
VOLUME = {9},
NUMBER = {9},
PAGES = {e106531},
URL = {http://dx.doi.org/10.1371/journal.pone.0106531},
NOTE = {http://arxiv.org/abs/1201.3722},
KEYWORDS = {explicit network, from triplets, heuristic, level k phylogenetic network, phylogenetic network, phylogeny, Program TripNet, reconstruction, software}
}

5

Sven Herrmann and Vincent Moulton. Computing the blocks of a quasi-median graph. In DAM, Vol. 179:129-138, 2014.
Keywords: abstract network, from sequences, phylogenetic network, phylogeny, polynomial, Program QuasiDec, quasi-median network, reconstruction.
Note: http://arxiv.org/abs/1206.6135.

@Article{HerrmannMoulton2014,
AUTHOR = {Herrmann, Sven and Moulton, Vincent},
TITLE = {Computing the blocks of a quasi-median graph},
YEAR = {2014},
JOURNAL = {DAM},
VOLUME = {179},
PAGES = {129-138},
URL = {http://dx.doi.org/10.1016/j.dam.2014.07.013},
NOTE = {http://arxiv.org/abs/1206.6135},
KEYWORDS = {abstract network, from sequences, phylogenetic network, phylogeny, polynomial, Program QuasiDec, quasi-median network, reconstruction}
}

6

Leo van Iersel and Vincent Moulton. Trinets encode tree-child and level-2 phylogenetic networks. In JOMB, Vol. 68(7):1707-1729, 2014.
Keywords: explicit network, from subnetworks, from trinets, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1210.0362.

Toggle abstract

@Article{IerselMoulton2014,
AUTHOR = {van Iersel, Leo and Moulton, Vincent},
TITLE = {Trinets encode tree-child and level-2 phylogenetic networks},
YEAR = {2014},
JOURNAL = {JOMB},
VOLUME = {68},
NUMBER = {7},
PAGES = {1707-1729},
URL = {http://dx.doi.org/10.1007/s00285-013-0683-5},
NOTE = {http://arxiv.org/abs/1210.0362},
KEYWORDS = {explicit network, from subnetworks, from trinets, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction}
}

7

Anthony Labarre and Sicco Verwer. Merging partially labelled trees: hardness and a declarative programming solution. In TCBB, Vol. 11(2):389-397, 2014.
Keywords: abstract network, from unrooted trees, heuristic, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: https://hal-upec-upem.archives-ouvertes.fr/hal-00855669.

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@Article{LabarreVerwer2014,
AUTHOR = {Labarre, Anthony and Verwer, Sicco},
TITLE = {Merging partially labelled trees: hardness and a declarative programming solution},
YEAR = {2014},
JOURNAL = {TCBB},
VOLUME = {11},
NUMBER = {2},
PAGES = {389-397},
URL = {http://dx.doi.org/10.1109/TCBB.2014.2307200},
NOTE = {https://hal-upec-upem.archives-ouvertes.fr/hal-00855669},
KEYWORDS = {abstract network, from unrooted trees, heuristic, NP complete, phylogenetic network, phylogeny, reconstruction}
}

8

Judith Keijsper and Rudi Pendavingh. Reconstructing a phylogenetic level-1 network from quartets. In BMB, Vol. 76(10):2517-2541, 2014.
Keywords: explicit network, from quartets, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://arxiv.org/abs/1308.5206.

@Article{KeijsperPendavingh2014,
AUTHOR = {Keijsper, Judith and Pendavingh, Rudi},
TITLE = {Reconstructing a phylogenetic level-1 network from quartets},
YEAR = {2014},
JOURNAL = {BMB},
VOLUME = {76},
NUMBER = {10},
PAGES = {2517-2541},
URL = {http://dx.doi.org/10.1007/s11538-014-0022-z},
NOTE = {http://arxiv.org/abs/1308.5206},
KEYWORDS = {explicit network, from quartets, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction}
}

9

Leo van Iersel and Steven Kelk. Kernelizations for the hybridization number problem on multiple nonbinary trees. In WG14, Vol. 8747:299-311 of LNCS, springer, 2014.
Keywords: explicit network, from rooted trees, kernelization, minimum number, phylogenetic network, phylogeny, Program Treeduce, reconstruction.
Note: http://arxiv.org/abs/1311.4045.

@InProceedings{IerselKelk2014,
AUTHOR = {van Iersel, Leo and Kelk, Steven},
TITLE = {Kernelizations for the hybridization number problem on multiple nonbinary trees},
YEAR = {2014},
BOOKTITLE = {WG14},
VOLUME = {8747},
PAGES = {299-311},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-319-12340-0_25},
NOTE = {http://arxiv.org/abs/1311.4045},
KEYWORDS = {explicit network, from rooted trees, kernelization, minimum number, phylogenetic network, phylogeny, Program Treeduce, reconstruction}
}

10

Jesper Jansson and Andrzej Lingas. Computing the rooted triplet distance between galled trees by counting triangles. In Journal of Discrete Algorithms, Vol. 25:66-78, 2014.
Keywords: distance between networks, explicit network, from network, galled network, phylogenetic network, phylogeny, polynomial, triplet distance.

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@Article{JanssonLingas2014,
AUTHOR = {Jansson, Jesper and Lingas, Andrzej},
TITLE = {Computing the rooted triplet distance between galled trees by counting triangles},
YEAR = {2014},
JOURNAL = {Journal of Discrete Algorithms},
VOLUME = {25},
PAGES = {66-78},
URL = {http://dx.doi.org/10.1016/j.jda.2013.10.002},
KEYWORDS = {distance between networks, explicit network, from network, galled network, phylogenetic network, phylogeny, polynomial, triplet distance}
}

11

Ward C Wheeler. Phyletic groups on networks. In Cladistics, Vol. 30(4):447-451, 2014.
Keywords: explicit network, from network, phylogenetic network, phylogeny.
Note: http://dx.doi.org/10.1111/cla.12062.

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@Article{Wheeler2014,
AUTHOR = {Wheeler, Ward C},
TITLE = {Phyletic groups on networks},
YEAR = {2014},
JOURNAL = {Cladistics},
VOLUME = {30},
NUMBER = {4},
PAGES = {447-451},
URL = {http://dx.doi.org/10.1111/cla.12062},
NOTE = {http://dx.doi.org/10.1111/cla.12062},
KEYWORDS = {explicit network, from network, phylogenetic network, phylogeny}
}

12

Sarah Bastkowski, Andreas Spillner and Vincent Moulton. Fishing for minimum evolution trees with Neighbor-Nets. In IPL, Vol. 114(1-2):3-18, 2014.
Keywords: circular split system, from distances, NeighborNet, phylogeny, polynomial.

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@Article{BSM2014,
AUTHOR = {Bastkowski, Sarah and Spillner, Andreas and Moulton, Vincent},
TITLE = {Fishing for minimum evolution trees with Neighbor-Nets},
YEAR = {2014},
JOURNAL = {IPL},
VOLUME = {114},
NUMBER = {1-2},
PAGES = {3-18},
URL = {http://dx.doi.org/10.1016/j.ipl.2013.10.003},
KEYWORDS = {circular split system, from distances, NeighborNet, phylogeny, polynomial}
}

13

Lavanya Kannan and Ward C Wheeler. Exactly Computing the Parsimony Scores on Phylogenetic Networks Using Dynamic Programming. In JCB, Vol. 21(4):303-319, 2014.
Keywords: explicit network, exponential algorithm, from network, from sequences, parsimony, phylogenetic network, phylogeny, reconstruction.

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@Article{KannanWheeler2014,
AUTHOR = {Kannan, Lavanya and Wheeler, Ward C},
TITLE = {Exactly Computing the Parsimony Scores on Phylogenetic Networks Using Dynamic Programming},
YEAR = {2014},
JOURNAL = {JCB},
VOLUME = {21},
NUMBER = {4},
PAGES = {303-319},
URL = {http://dx.doi.org/10.1089/cmb.2013.0134},
KEYWORDS = {explicit network, exponential algorithm, from network, from sequences, parsimony, phylogenetic network, phylogeny, reconstruction}
}

14

Jialiang Yang, Stefan Grünewald, Yifei Xu and Xiu-Feng Wan. Quartet-based methods to reconstruct phylogenetic networks. In BMC Systems Biology, Vol. 80(21), 2014.
Keywords: abstract network, from quartets, phylogenetic network, phylogeny, Program QuartetMethods, Program QuartetNet, Program SplitsTree, reconstruction.
Note: http://dx.doi.org/10.1186/1752-0509-8-21 .

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@Article{YGXW2014,
AUTHOR = {Yang, Jialiang and Gr{\~A}�newald, Stefan and Xu, Yifei and Wan, Xiu-Feng},
TITLE = {Quartet-based methods to reconstruct phylogenetic networks},
YEAR = {2014},
JOURNAL = {BMC Systems Biology},
VOLUME = {80},
NUMBER = {21},
URL = {http://dx.doi.org/10.1186/1752-0509-8-21},
NOTE = {http://dx.doi.org/10.1186/1752-0509-8-21 },
KEYWORDS = {abstract network, from quartets, phylogenetic network, phylogeny, Program QuartetMethods, Program QuartetNet, Program SplitsTree, reconstruction}
}

15

Ran Libeskind-Hadas, Yi-Chieh Wu, Mukul S. Bansal and Manolis Kellis. Pareto-optimal phylogenetic tree reconciliation. In ISMB14, Vol. 30:i87-i95 of BIO, 2014.
Keywords: duplication, lateral gene transfer, loss, phylogenetic network, phylogeny, polynomial, Program Xscape, reconstruction.
Note: http://dx.doi.org/10.1093/bioinformatics/btu289.

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@InProceedings{LWBK2014,
AUTHOR = {Libeskind-Hadas, Ran and Wu, Yi-Chieh and Bansal, Mukul S. and Kellis, Manolis},
TITLE = {Pareto-optimal phylogenetic tree reconciliation},
YEAR = {2014},
BOOKTITLE = {ISMB14},
VOLUME = {30},
PAGES = {i87-i95},
SERIES = {BIO},
URL = {http://dx.doi.org/10.1093/bioinformatics/btu289},
NOTE = {http://dx.doi.org/10.1093/bioinformatics/btu289},
KEYWORDS = {duplication, lateral gene transfer, loss, phylogenetic network, phylogeny, polynomial, Program Xscape, reconstruction}
}

16

Kevin J. Liu, Jingxuan Dai, Kathy Truong, Ying Song, Michael H. Kohn and Luay Nakhleh. An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes. In PLoS ONE, Vol. 10(6):e1003649, 2014.
Keywords: explicit network, from network, phylogenetic network, phylogeny, Program PhyloNet-HMM.
Note: http://arxiv.org/abs/1310.7989.

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@Article{LDTSKN2014,
AUTHOR = {Liu, Kevin J. and Dai, Jingxuan and Truong, Kathy and Song, Ying and Kohn, Michael H. and Nakhleh, Luay},
TITLE = {An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes},
YEAR = {2014},
JOURNAL = {PLoS ONE},
VOLUME = {10},
NUMBER = {6},
PAGES = {e1003649},
URL = {http://dx.doi.org/10.1371/journal.pcbi.1003649},
NOTE = {http://arxiv.org/abs/1310.7989},
KEYWORDS = {explicit network, from network, phylogenetic network, phylogeny, Program PhyloNet-HMM}
}

17

David A. Morrison. Phylogenetic Networks: A Review of Methods to Display Evolutionary History. In Annual Research & Review in Biology, Vol. 4(10):1518-1543, 2014.
Keywords: explicit network, phylogenetic network, phylogeny, reconstruction, survey.

@Article{Morrison2014a,
AUTHOR = {Morrison, David A.},
TITLE = {Phylogenetic Networks: A Review of Methods to Display Evolutionary History},
YEAR = {2014},
JOURNAL = {Annual Research {\&} Review in Biology},
VOLUME = {4},
NUMBER = {10},
PAGES = {1518-1543},
URL = {https://dx.doi.org/10.9734/ARRB/2014/8230},
KEYWORDS = {explicit network, phylogenetic network, phylogeny, reconstruction, survey}
}

18

David A. Morrison. Rooted Phylogenetic Networks for Exploratory Data Analysis. In Advances in Research, Vol. 2(3):145-152, 2014.
Keywords: abstract network, explicit network, phylogenetic network, reconstruction.

@Article{Morrison2014b,
AUTHOR = {Morrison, David A.},
TITLE = {Rooted Phylogenetic Networks for Exploratory Data Analysis},
YEAR = {2014},
JOURNAL = {Advances in Research},
VOLUME = {2},
NUMBER = {3},
PAGES = {145-152},
URL = {https://dx.doi.org/10.9734/AIR/2014/8485},
KEYWORDS = {abstract network, explicit network, phylogenetic network, reconstruction}
}

19

David A. Morrison. Next generation sequencing and phylogenetic networks. In EMBnet.journal, Vol. 20(e760):1-4, 2014.
Keywords: abstract network, from NGS data, phylogenetic network, phylogeny, Program SplitsTree, reconstruction.

@Article{Morrison2014c,
AUTHOR = {Morrison, David A.},
TITLE = {Next generation sequencing and phylogenetic networks},
YEAR = {2014},
JOURNAL = {EMBnet.journal},
VOLUME = {20},
NUMBER = {e760},
PAGES = {1-4},
URL = {http://dx.doi.org/10.14806/ej.20.0.760},
KEYWORDS = {abstract network, from NGS data, phylogenetic network, phylogeny, Program SplitsTree, reconstruction}
}

20

Dan Gusfield. ReCombinatorics: The Algorithmics of Ancestral Recombination Graphs and Explicit Phylogenetic Networks. MIT Press, 2014.
Keywords: ARG, explicit network, phylogenetic network, phylogeny, survey.
Note: http://mitpress.mit.edu/books/recombinatorics.

@Book{Gusfield2014,
AUTHOR = {Gusfield, Dan},
TITLE = {ReCombinatorics: The Algorithmics of Ancestral Recombination Graphs and Explicit Phylogenetic Networks},
YEAR = {2014},
PUBLISHER = {MIT Press},
NOTE = {http://mitpress.mit.edu/books/recombinatorics},
KEYWORDS = {ARG, explicit network, phylogenetic network, phylogeny, survey}
}

21

Josh Voorkamp né Collins. Untangling Evolution. PhD thesis, University of Otago, New Zealand, 2014.
Keywords: agreement forest, explicit network, from rooted trees, generation, phylogenetic network, phylogeny, reconstruction.
Note: http://otago.ourarchive.ac.nz/handle/10523/4802.

@PhdThesis{Voorkamp2014,
AUTHOR = {Voorkamp n{\~A}� Collins, Josh},
TITLE = {Untangling Evolution},
YEAR = {2014},
SCHOOL = {University of Otago, New Zealand},
NOTE = {http://otago.ourarchive.ac.nz/handle/10523/4802},
KEYWORDS = {agreement forest, explicit network, from rooted trees, generation, phylogenetic network, phylogeny, reconstruction}
}

22

Vladimir Makarenkov, Alix Boc and Pierre Legendre. A New Algorithm for Inferring Hybridization Events Based on the Detection of Horizontal Gene Transfers. In Fuad Aleskerov, Boris Goldengorin and Panos M. Pardalos editors, Clusters, Orders, and Trees: Methods and Applications, Vol. 92 of Springer Optimization and Its Applications, Springer, 2014.
Keywords: explicit network, phylogenetic network, phylogeny, reconstruction.

@InBook{MBL2014,
AUTHOR = {Makarenkov, Vladimir and Boc, Alix and Legendre, Pierre},
TITLE = {A New Algorithm for Inferring Hybridization Events Based on the Detection of Horizontal Gene Transfers},
YEAR = {2014},
BOOKTITLE = {Clusters, Orders, and Trees: Methods and Applications},
VOLUME = {92},
EDITOR = {Aleskerov, Fuad and Goldengorin, Boris and Pardalos, Panos M.},
SERIES = {Springer Optimization and Its Applications},
PUBLISHER = {Springer},
URL = {http://dx.doi.org/10.1007/978-1-4939-0742-7_17},
KEYWORDS = {explicit network, phylogenetic network, phylogeny, reconstruction}
}

23

Leo van Iersel, Steven Kelk, Nela Lekic and Celine Scornavacca. A practical approximation algorithm for solving massive instances of hybridization number for binary and nonbinary trees. In BMCB, Vol. 15(127):1-12, 2014.
Keywords: agreement forest, approximation, explicit network, from rooted trees, phylogenetic network, phylogeny, Program CycleKiller, Program TerminusEst, reconstruction.
Note: http://dx.doi.org/10.1186/1471-2105-15-127.

@Article{IKLS2014b,
AUTHOR = {van Iersel, Leo and Kelk, Steven and Lekic, Nela and Scornavacca, Celine},
TITLE = {A practical approximation algorithm for solving massive instances of hybridization number for binary and nonbinary trees},
YEAR = {2014},
JOURNAL = {BMCB},
VOLUME = {15},
NUMBER = {127},
PAGES = {1-12},
URL = {http://dx.doi.org/10.1186/1471-2105-15-127},
NOTE = {http://dx.doi.org/10.1186/1471-2105-15-127},
KEYWORDS = {agreement forest, approximation, explicit network, from rooted trees, phylogenetic network, phylogeny, Program CycleKiller, Program TerminusEst, reconstruction}
}

24

Yi-Chieh Wu. Computational evolutionary genomics : phylogenomic models spanning domains, genes, individuals, and species. PhD thesis, Massachusetts Institute of Technology, U.S.A., 2014.
Keywords: duplication, from sequences, from species tree, lateral gene transfer, loss, phylogeny, Program TreeFix-DTL, reconstruction.
Note: http://hdl.handle.net/1721.1/87937.

@PhdThesis{Wu2014,
AUTHOR = {Wu, Yi-Chieh},
TITLE = {Computational evolutionary genomics : phylogenomic models spanning domains, genes, individuals, and species},
YEAR = {2014},
SCHOOL = {Massachusetts Institute of Technology, U.S.A.},
URL = {http://hdl.handle.net/1721.1/87937},
NOTE = {http://hdl.handle.net/1721.1/87937},
KEYWORDS = {duplication, from sequences, from species tree, lateral gene transfer, loss, phylogeny, Program TreeFix-DTL, reconstruction}
}

25

Monika Balvociute, Andreas Spillner and Vincent Moulton. FlatNJ: A Novel Network-Based Approach to Visualize Evolutionary and Biogeographical Relationships. In Systematic Biology, Vol. 63(3):383-396, 2014.
Keywords: abstract network, flat, phylogenetic network, phylogeny, Program FlatNJ, Program SplitsTree, split network.
Note: http://dx.doi.org/10.1093/sysbio/syu001.

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@Article{BSM2014b,
AUTHOR = {Balvociute, Monika and Spillner, Andreas and Moulton, Vincent},
TITLE = {FlatNJ: A Novel Network-Based Approach to Visualize Evolutionary and Biogeographical Relationships},
YEAR = {2014},
JOURNAL = {Systematic Biology},
VOLUME = {63},
NUMBER = {3},
PAGES = {383-396},
URL = {http://dx.doi.org/10.1093/sysbio/syu001},
NOTE = {http://dx.doi.org/10.1093/sysbio/syu001},
KEYWORDS = {abstract network, flat, phylogenetic network, phylogeny, Program FlatNJ, Program SplitsTree, split network}
}

26

Johann-Mattis List, Shijulal Nelson-Sathi, Hans Geisler and William Martin. Networks of lexical borrowing and lateral gene transfer in language and genome evolution. In BioEssays, Vol. 36(2):141-150, 2014.
Keywords: explicit network, minimal lateral network, phylogenetic network, Program lingpy.
Note: http://dx.doi.org/10.1002/bies.201300096.

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@Article{LNGM2014,
AUTHOR = {List, Johann-Mattis and Nelson-Sathi, Shijulal and Geisler, Hans and Martin, William},
TITLE = {Networks of lexical borrowing and lateral gene transfer in language and genome evolution},
YEAR = {2014},
JOURNAL = {BioEssays},
VOLUME = {36},
NUMBER = {2},
PAGES = {141-150},
URL = {http://dx.doi.org/10.1002/bies.201300096},
NOTE = {http://dx.doi.org/10.1002/bies.201300096},
KEYWORDS = {explicit network, minimal lateral network, phylogenetic network, Program lingpy}
}

27

Benjamin Albrecht. Computing Hybridization Networks for Multiple Rooted Binary Phylogenetic Trees by Maximum Acyclic Agreement Forests. 2014.
Keywords: agreement forest, from rooted trees, minimum number, phylogenetic network, phylogeny, polynomial, Program Hybroscale, reconstruction.
Note: http://arxiv.org/abs/1408.3044.

@Misc{Albrecht2014,
AUTHOR = {Albrecht, Benjamin},
TITLE = {Computing Hybridization Networks for Multiple Rooted Binary Phylogenetic Trees by Maximum Acyclic Agreement Forests},
YEAR = {2014},
NOTE = {http://arxiv.org/abs/1408.3044},
KEYWORDS = {agreement forest, from rooted trees, minimum number, phylogenetic network, phylogeny, polynomial, Program Hybroscale, reconstruction}
}

28

Puspal Bhabak and Asish Mukhopadhyay. A 3-factor approximation algorithm for a Minimum Acyclic Agreement Forest on k rooted, binary phylogenetic trees. 2014.
Keywords: agreement forest, approximation, explicit network, from rooted trees, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1407.7125.

@Misc{BhabakMukhopadhyay2014,
AUTHOR = {Bhabak, Puspal and Mukhopadhyay, Asish},
TITLE = {A 3-factor approximation algorithm for a Minimum Acyclic Agreement Forest on k rooted, binary phylogenetic trees},
YEAR = {2014},
NOTE = {http://arxiv.org/abs/1407.7125},
KEYWORDS = {agreement forest, approximation, explicit network, from rooted trees, phylogenetic network, phylogeny, reconstruction}
}

29

Zhijiang Li. Fixed-Parameter Algorithm for Hybridization Number of Two Multifurcating Trees. Master's thesis, Dalhousie University, Canada, 2014.
Keywords: agreement forest, explicit network, FPT, from rooted trees, minimum number, phylogenetic network, phylogeny, reconstruction.
Note: http://hdl.handle.net/10222/53976.

@MastersThesis{Li2014,
AUTHOR = {Li, Zhijiang},
TITLE = {Fixed-Parameter Algorithm for Hybridization Number of Two Multifurcating Trees},
YEAR = {2014},
SCHOOL = {Dalhousie University, Canada},
URL = {http://hdl.handle.net/10222/53976},
NOTE = {http://hdl.handle.net/10222/53976},
KEYWORDS = {agreement forest, explicit network, FPT, from rooted trees, minimum number, phylogenetic network, phylogeny, reconstruction}
}

30

Juan Wang. A new algorithm to construct phylogenetic networks from trees. In Genetics and Molecular Research, Vol. 13(1):1456-1464, 2014.
Keywords: explicit network, from clusters, heuristic, phylogenetic network, Program LNetwork, Program QuickCass, reconstruction.
Note: http://dx.doi.org/10.4238/2014.March.6.4.

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@Article{Wang2014,
AUTHOR = {Wang, Juan},
TITLE = {A new algorithm to construct phylogenetic networks from trees},
YEAR = {2014},
JOURNAL = {Genetics and Molecular Research},
VOLUME = {13},
NUMBER = {1},
PAGES = {1456-1464},
URL = {http://dx.doi.org/10.4238/2014.March.6.4},
NOTE = {http://dx.doi.org/10.4238/2014.March.6.4},
KEYWORDS = {explicit network, from clusters, heuristic, phylogenetic network, Program LNetwork, Program QuickCass, reconstruction}
}

31

Matthieu Willems, Nadia Tahiri and Vladimir Makarenkov. A new efficient algorithm for inferring explicit hybridization networks following the Neighbor-Joining principle. In JBCB, Vol. 12(5), 2014.
Keywords: explicit network, from distances, heuristic, phylogenetic network, phylogeny, reconstruction.

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@Article{WTM2014,
AUTHOR = {Willems, Matthieu and Tahiri, Nadia and Makarenkov, Vladimir},
TITLE = {A new efficient algorithm for inferring explicit hybridization networks following the Neighbor-Joining principle},
YEAR = {2014},
JOURNAL = {JBCB},
VOLUME = {12},
NUMBER = {5},
URL = {http://dx.doi.org/10.1142/S0219720014500243},
KEYWORDS = {explicit network, from distances, heuristic, phylogenetic network, phylogeny, reconstruction}
}

32

Paul Cordue, Simone Linz and Charles Semple. Phylogenetic Networks that Display a Tree Twice. In BMB, Vol. 76(10):2664-2679, 2014.
Keywords: from rooted trees, normal network, phylogenetic network, phylogeny, reconstruction, tree-child network.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/CLS14.pdf.

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@Article{CLS2014,
AUTHOR = {Cordue, Paul and Linz, Simone and Semple, Charles},
TITLE = {Phylogenetic Networks that Display a Tree Twice},
YEAR = {2014},
JOURNAL = {BMB},
VOLUME = {76},
NUMBER = {10},
PAGES = {2664-2679},
URL = {http://dx.doi.org/10.1007/s11538-014-0032-x},
NOTE = {http://www.math.canterbury.ac.nz/~c.semple/papers/CLS14.pdf},
KEYWORDS = {from rooted trees, normal network, phylogenetic network, phylogeny, reconstruction, tree-child network}
}

33

Riccardo Dondi and Yuri Pirola. Beyond Evolutionary Trees. In Ming-Yang Kao editor, Encyclopedia of Algorithms, Pages 1-7, Springer, 2014.
Keywords: explicit network, phylogenetic network, phylogeny, reconstruction, survey.

@InBook{DondiPirola2014,
AUTHOR = {Dondi, Riccardo and Pirola, Yuri},
TITLE = {Beyond Evolutionary Trees},
YEAR = {2014},
BOOKTITLE = {Encyclopedia of Algorithms},
PAGES = {1-7},
EDITOR = {Kao, Ming-Yang},
PUBLISHER = {Springer},
URL = {http://dx.doi.org/10.1007/978-3-642-27848-8_599-1},
KEYWORDS = {explicit network, phylogenetic network, phylogeny, reconstruction, survey}
}

34

Josh Voorkamp né Collins. Maximal Acyclic Agreement Forests. In JCB, Vol. 21(10):723-731, 2014.
Keywords: agreement forest, explicit network, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction.

@Article{Voorkamp2014b,
AUTHOR = {Voorkamp n{\~A}� Collins, Josh},
TITLE = {Maximal Acyclic Agreement Forests},
YEAR = {2014},
JOURNAL = {JCB},
VOLUME = {21},
NUMBER = {10},
PAGES = {723-731},
URL = {http://dx.doi.org/10.1089/cmb.2014.0093},
KEYWORDS = {agreement forest, explicit network, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction}
}

35

Yun Yu. Models and Methods for Evolutionary Histories Involving Hybridization and Incomplete Lineage Sorting. PhD thesis, Rice University, U.S.A., 2014.
Keywords: hybridization, incomplete lineage sorting, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, software.
Note: http://hdl.handle.net/1911/77583.

@PhdThesis{Yu2014,
AUTHOR = {Yu, Yun},
TITLE = {Models and Methods for Evolutionary Histories Involving Hybridization and Incomplete Lineage Sorting},
YEAR = {2014},
SCHOOL = {Rice University, U.S.A.},
URL = {http://hdl.handle.net/1911/77583},
NOTE = {http://hdl.handle.net/1911/77583},
KEYWORDS = {hybridization, incomplete lineage sorting, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, software}
}

36

Yun Yu, Jianrong Dong, Kevin J. Liu and Luay Nakhleh. Maximum likelihood inference of reticulate evolutionary histories. In PNAS, Vol. 111(46):16448-16453, 2014.
Keywords: explicit network, likelihood, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1073/pnas.1407950111.

@Article{YDLN2014,
AUTHOR = {Yu, Yun and Dong, Jianrong and Liu, Kevin J. and Nakhleh, Luay},
TITLE = {Maximum likelihood inference of reticulate evolutionary histories},
YEAR = {2014},
JOURNAL = {PNAS},
VOLUME = {111},
NUMBER = {46},
PAGES = {16448-16453},
URL = {http://dx.doi.org/10.1073/pnas.1407950111},
NOTE = {http://dx.doi.org/10.1073/pnas.1407950111},
KEYWORDS = {explicit network, likelihood, phylogenetic network, phylogeny, reconstruction}
}

37

Julia Matsieva. A Static Formulation of the History Bound Problem. Master's thesis, UC Davis, 2014.
Keywords: bound, dynamic programming, explicit network, from binary characters, from clusters, phylogenetic network, phylogeny, polynomial.
Note: https://escholarship.org/uc/item/3741t064.

@MastersThesis{Matsieva2014,
AUTHOR = {Matsieva, Julia},
TITLE = {A Static Formulation of the History Bound Problem},
YEAR = {2014},
SCHOOL = {UC Davis},
URL = {https://escholarship.org/uc/item/3741t064},
NOTE = {https://escholarship.org/uc/item/3741t064},
KEYWORDS = {bound, dynamic programming, explicit network, from binary characters, from clusters, phylogenetic network, phylogeny, polynomial}
}

38

Joel Sjöstrand, Ali Tofigh, Vincent Daubin, Lars Arvestad, Bengt Sennblad and Jens Lagergren. A Bayesian Method for Analyzing Lateral Gene Transfer. In Systematic Biology, Vol. 63(3):409-420, 2014.
Keywords: bayesian, duplication, from rooted trees, from sequences, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program JPrIME-DLTRS, reconstruction.
Note: http://dx.doi.org/10.1093/sysbio/syu007.

@Article{STDASL2014,
AUTHOR = {Sj{\~A}�strand, Joel and Tofigh, Ali and Daubin, Vincent and Arvestad, Lars and Sennblad, Bengt and Lagergren, Jens},
TITLE = {A Bayesian Method for Analyzing Lateral Gene Transfer},
YEAR = {2014},
JOURNAL = {Systematic Biology},
VOLUME = {63},
NUMBER = {3},
PAGES = {409-420},
URL = {http://dx.doi.org/10.1093/sysbio/syu007},
NOTE = {http://dx.doi.org/10.1093/sysbio/syu007},
KEYWORDS = {bayesian, duplication, from rooted trees, from sequences, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program JPrIME-DLTRS, reconstruction}
}

39

Adrià Alcalà Mena, Mercè Llabrés, Francesc Rosselló and Pau Rullan. Tree-Child Cluster Networks. In Fundamenta Informaticae, Vol. 134(1-2):1-15, 2014.
Keywords: explicit network, from clusters, phylogenetic network, phylogeny, Program PhyloNetwork, reconstruction, tree-child network.

@Article{ALRR2014,
AUTHOR = {Alcal{\~A}� Mena, Adri{\~A}� and Llabr{\~A}�s, Merc{\~A}� and Rossell{\~A}�, Francesc and Rullan, Pau},
TITLE = {Tree-Child Cluster Networks},
YEAR = {2014},
JOURNAL = {Fundamenta Informaticae},
VOLUME = {134},
NUMBER = {1-2},
PAGES = {1-15},
URL = {http://dx.doi.org/10.3233/FI-2014-1087},
KEYWORDS = {explicit network, from clusters, phylogenetic network, phylogeny, Program PhyloNetwork, reconstruction, tree-child network}
}

40

David A. Morrison. Is the Tree of Life the Best Metaphor, Model, or Heuristic for Phylogenetics? In Systematic Biology, Vol. 63(4):628-638, 2014.
Keywords: abstract network, explicit network, phylogenetic network, phylogeny, survey.

@Article{Morrison2014,
AUTHOR = {Morrison, David A.},
TITLE = {Is the Tree of Life the Best Metaphor, Model, or Heuristic for Phylogenetics?},
YEAR = {2014},
JOURNAL = {Systematic Biology},
VOLUME = {63},
NUMBER = {4},
PAGES = {628-638},
URL = {http://dx.doi.org/10.1093/sysbio/syu026},
KEYWORDS = {abstract network, explicit network, phylogenetic network, phylogeny, survey}
}

41

Leo van Iersel, Celine Scornavacca and Steven Kelk. Exact reconciliation of undated trees. 2014.
Keywords: duplication, explicit network, integer linear programming, loss, phylogenetic network, phylogeny, Program ILPEACE, reconstruction.
Note: https://arxiv.org/abs/1410.7004.

@Misc{IerselScornavaccaKelk2014,
AUTHOR = {van Iersel, Leo and Scornavacca, Celine and Kelk, Steven},
TITLE = {Exact reconciliation of undated trees},
YEAR = {2014},
NOTE = {https://arxiv.org/abs/1410.7004},
KEYWORDS = {duplication, explicit network, integer linear programming, loss, phylogenetic network, phylogeny, Program ILPEACE, reconstruction}
}

2013

1

Katharina Huber and Vincent Moulton. Encoding and Constructing 1-Nested Phylogenetic Networks with Trinets. In ALG, Vol. 66(3):714-738, 2013.
Keywords: explicit network, from subnetworks, from trinets, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: http://arxiv.org/abs/1110.0728.

Toggle abstract

@Article{HuberMoulton2013,
AUTHOR = {Huber, Katharina and Moulton, Vincent},
TITLE = {Encoding and Constructing 1-Nested Phylogenetic Networks with Trinets},
YEAR = {2013},
JOURNAL = {ALG},
VOLUME = {66},
NUMBER = {3},
PAGES = {714-738},
URL = {http://dx.doi.org/10.1007/s00453-012-9659-x},
NOTE = {http://arxiv.org/abs/1110.0728},
KEYWORDS = {explicit network, from subnetworks, from trinets, phylogenetic network, phylogeny, reconstruction, uniqueness}
}

2

Leo van Iersel and Simone Linz. A quadratic kernel for computing the hybridization number of multiple trees. In IPL, Vol. 113:318-323, 2013.
Keywords: explicit network, FPT, from rooted trees, kernelization, minimum number, phylogenetic network, phylogeny, Program Clustistic, Program MaafB, Program PIRN, reconstruction.
Note: http://arxiv.org/abs/1203.4067, poster.

Toggle abstract

@Article{IerselLinz2013,
AUTHOR = {van Iersel, Leo and Linz, Simone},
TITLE = {A quadratic kernel for computing the hybridization number of multiple trees},
YEAR = {2013},
JOURNAL = {IPL},
VOLUME = {113},
PAGES = {318-323},
URL = {http://dx.doi.org/10.1016/j.ipl.2013.02.010},
NOTE = {http://arxiv.org/abs/1203.4067, poster},
KEYWORDS = {explicit network, FPT, from rooted trees, kernelization, minimum number, phylogenetic network, phylogeny, Program Clustistic, Program MaafB, Program PIRN, reconstruction}
}

3

Chris Whidden, Robert G. Beiko and Norbert Zeh. Fixed-Parameter Algorithms for Maximum Agreement Forests. In SICOMP, Vol. 42(4):1431-1466, 2013.
Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, SPR distance.
Note: http://arxiv.org/abs/1108.2664, slides.

Toggle abstract

@Article{WBZ2013,
AUTHOR = {Whidden, Chris and Beiko, Robert G. and Zeh, Norbert},
TITLE = {Fixed-Parameter Algorithms for Maximum Agreement Forests},
YEAR = {2013},
JOURNAL = {SICOMP},
VOLUME = {42},
NUMBER = {4},
PAGES = {1431-1466},
URL = {http://dx.doi.org/10.1137/110845045},
NOTE = {http://arxiv.org/abs/1108.2664, slides},
KEYWORDS = {agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, SPR distance}
}

4

Stefan Grünewald, Andreas Spillner, Sarah Bastkowski, Anja Bögershausen and Vincent Moulton. SuperQ: Computing Supernetworks from Quartets. In TCBB, Vol. 10(1):151-160, 2013.
Keywords: abstract network, circular split system, from quartets, heuristic, phylogenetic network, phylogeny, Program QNet, Program SplitsTree, Program SuperQ, software, split network.

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@Article{GSBBM2013,
AUTHOR = {Gr{\~A}�newald, Stefan and Spillner, Andreas and Bastkowski, Sarah and B{\~A}�gershausen, Anja and Moulton, Vincent},
TITLE = {SuperQ: Computing Supernetworks from Quartets},
YEAR = {2013},
JOURNAL = {TCBB},
VOLUME = {10},
NUMBER = {1},
PAGES = {151-160},
URL = {http://dx.doi.org/10.1109/TCBB.2013.8},
KEYWORDS = {abstract network, circular split system, from quartets, heuristic, phylogenetic network, phylogeny, Program QNet, Program SplitsTree, Program SuperQ, software, split network}
}

5

Teresa Piovesan and Steven Kelk. A simple fixed parameter tractable algorithm for computing the hybridization number of two (not necessarily binary) trees. In TCBB, Vol. 10(1):18-25, 2013.
Keywords: FPT, from rooted trees, phylogenetic network, phylogeny, Program TerminusEst, reconstruction.
Note: http://arxiv.org/abs/1207.6090.

Toggle abstract

@Article{PiovesanKelk2013,
AUTHOR = {Piovesan, Teresa and Kelk, Steven},
TITLE = {A simple fixed parameter tractable algorithm for computing the hybridization number of two (not necessarily binary) trees},
YEAR = {2013},
JOURNAL = {TCBB},
VOLUME = {10},
NUMBER = {1},
PAGES = {18-25},
URL = {http://dx.doi.org/10.1109/TCBB.2012.134},
NOTE = {http://arxiv.org/abs/1207.6090},
KEYWORDS = {FPT, from rooted trees, phylogenetic network, phylogeny, Program TerminusEst, reconstruction}
}

6

Stephen J. Willson. Reconstruction of certain phylogenetic networks from their tree-average distances. In BMB, Vol. 75(10):1840-1878, 2013.
Keywords: explicit network, from distances, galled tree, normal network, phylogenetic network, phylogeny, unicyclic network.
Note: http://www.public.iastate.edu/~swillson/Tree-AverageReconPaper9.pdf.

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@Article{Willson2013,
AUTHOR = {Willson, Stephen J.},
TITLE = {Reconstruction of certain phylogenetic networks from their tree-average distances},
YEAR = {2013},
JOURNAL = {BMB},
VOLUME = {75},
NUMBER = {10},
PAGES = {1840-1878},
URL = {http://dx.doi.org/10.1007/s11538-013-9872-z},
NOTE = {http://www.public.iastate.edu/~swillson/Tree-AverageReconPaper9.pdf},
KEYWORDS = {explicit network, from distances, galled tree, normal network, phylogenetic network, phylogeny, unicyclic network}
}

7

Peter J. Humphries, Simone Linz and Charles Semple. On the complexity of computing the temporal hybridization number for two phylogenies. In DAM, Vol. 161:871-880, 2013.
Keywords: agreement forest, APX hard, characterization, from rooted trees, hybridization, NP complete, phylogenetic network, phylogeny, reconstruction, time consistent network.
Note: http://ab.inf.uni-tuebingen.de/people/linz/publications/TAFapx.pdf.

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@Article{HLS2013,
AUTHOR = {Humphries, Peter J. and Linz, Simone and Semple, Charles},
TITLE = {On the complexity of computing the temporal hybridization number for two phylogenies},
YEAR = {2013},
JOURNAL = {DAM},
VOLUME = {161},
PAGES = {871-880},
URL = {http://dx.doi.org/10.1016/j.dam.2012.11.022},
NOTE = {http://ab.inf.uni-tuebingen.de/people/linz/publications/TAFapx.pdf},
KEYWORDS = {agreement forest, APX hard, characterization, from rooted trees, hybridization, NP complete, phylogenetic network, phylogeny, reconstruction, time consistent network}
}

8

Yufeng Wu. An Algorithm for Constructing Parsimonious Hybridization Networks with Multiple Phylogenetic Trees. In RECOMB13, Vol. 7821:291-303 of LNCS, springer, 2013.
Keywords: explicit network, exponential algorithm, from rooted trees, phylogenetic network, phylogeny, Program PIRN, reconstruction.
Note: http://www.engr.uconn.edu/~ywu/Papers/ExactNetRecomb2013.pdf.

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@InProceedings{Wu2013,
AUTHOR = {Wu, Yufeng},
TITLE = {An Algorithm for Constructing Parsimonious Hybridization Networks with Multiple Phylogenetic Trees},
YEAR = {2013},
BOOKTITLE = {RECOMB13},
VOLUME = {7821},
PAGES = {291-303},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-642-37195-0_29},
NOTE = {http://www.engr.uconn.edu/~ywu/Papers/ExactNetRecomb2013.pdf},
KEYWORDS = {explicit network, exponential algorithm, from rooted trees, phylogenetic network, phylogeny, Program PIRN, reconstruction}
}

9

Mukul S. Bansal, Eric J. Alm and Manolis Kellis. Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss. In RECOMB13, Vol. 7821:1-13 of LNCS, springer, 2013.
Keywords: duplication, from rooted trees, from species tree, loss, phylogenetic network, phylogeny, polynomial, Program RANGER-DTL, reconstruction.
Note: http://people.csail.mit.edu/mukul/Bansal_RECOMB2013.pdf.

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@InProceedings{BAK2013,
AUTHOR = {Bansal, Mukul S. and Alm, Eric J. and Kellis, Manolis},
TITLE = {Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss},
YEAR = {2013},
BOOKTITLE = {RECOMB13},
VOLUME = {7821},
PAGES = {1-13},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-642-37195-0_1},
NOTE = {http://people.csail.mit.edu/mukul/Bansal_RECOMB2013.pdf},
KEYWORDS = {duplication, from rooted trees, from species tree, loss, phylogenetic network, phylogeny, polynomial, Program RANGER-DTL, reconstruction}
}

10

Miguel Arenas. Computer programs and methodologies for the simulation of DNA sequence data with recombination. In Frontiers in Genetics, Vol. 4(9), 2013.
Keywords: explicit network, phylogenetic network, phylogeny, simulation.
Note: http://dx.doi.org/10.3389%2Ffgene.2013.00009.

@Article{Arenas2013,
AUTHOR = {Arenas, Miguel},
TITLE = {Computer programs and methodologies for the simulation of DNA sequence data with recombination},
YEAR = {2013},
JOURNAL = {Frontiers in Genetics},
VOLUME = {4},
NUMBER = {9},
URL = {http://dx.doi.org/10.3389%2Ffgene.2013.00009},
NOTE = {http://dx.doi.org/10.3389%2Ffgene.2013.00009},
KEYWORDS = {explicit network, phylogenetic network, phylogeny, simulation}
}

11

Sha Zhu, James H. Degnan and Bjarki Eldon. Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees. 2013.
Keywords: explicit network, from network, phylogenetic network, phylogeny, Program Hybrid-Lambda, simulation, software.
Note: http://arxiv.org/abs/1303.0673.

@Misc{ZDE2013,
AUTHOR = {Zhu, Sha and Degnan, James H. and Eldon, Bjarki},
TITLE = {Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees},
YEAR = {2013},
NOTE = {http://arxiv.org/abs/1303.0673},
KEYWORDS = {explicit network, from network, phylogenetic network, phylogeny, Program Hybrid-Lambda, simulation, software}
}

12

Jialiang Yang, Stefan Grünewald and Xiu-Feng Wan. Quartet-Net: A Quartet Based Method to Reconstruct Phylogenetic Networks. In MBE, Vol. 30(5):1206-1217, 2013.
Keywords: from quartets, phylogenetic network, phylogeny, Program QuartetNet, reconstruction.

Toggle abstract

@Article{YGW2013,
AUTHOR = {Yang, Jialiang and Gr{\~A}�newald, Stefan and Wan, Xiu-Feng},
TITLE = {Quartet-Net: A Quartet Based Method to Reconstruct Phylogenetic Networks},
YEAR = {2013},
JOURNAL = {MBE},
VOLUME = {30},
NUMBER = {5},
PAGES = {1206-1217},
URL = {http://dx.doi.org/10.1093/molbev/mst040},
KEYWORDS = {from quartets, phylogenetic network, phylogeny, Program QuartetNet, reconstruction}
}

13

Thi-Hau Nguyen, Vincent Ranwez, Stéphanie Pointet, Anne-Muriel Chifolleau Arigon, Jean-Philippe Doyon and Vincent Berry. Reconciliation and local gene tree rearrangement can be of mutual profit. In ALMOB, Vol. 8(12), 2013.
Keywords: duplication, explicit network, from rooted trees, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program Mowgli, Program MowgliNNI, Program Prunier, reconstruction, software.

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@Article{NVPCDB2013,
AUTHOR = {Nguyen, Thi-Hau and Ranwez, Vincent and Pointet, St{\~A}�phanie and Chifolleau Arigon, Anne-Muriel and Doyon, Jean-Philippe and Berry, Vincent},
TITLE = {Reconciliation and local gene tree rearrangement can be of mutual profit},
YEAR = {2013},
JOURNAL = {ALMOB},
VOLUME = {8},
NUMBER = {12},
URL = {http://dx.doi.org/10.1186/1748-7188-8-12},
KEYWORDS = {duplication, explicit network, from rooted trees, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program Mowgli, Program MowgliNNI, Program Prunier, reconstruction, software}
}

14

Hoa Vu, Francis Chin, Wing-Kai Hon, Henry Leung, Kunihiko Sadakane, Wing-Kin Sung and Siu-Ming Yiu. Reconstructing k-Reticulated Phylogenetic Network from a Set of Gene Trees. In ISBRA13, Vol. 7875:112-124 of LNCS, springer, 2013.
Keywords: from rooted trees, k-reticulated, phylogenetic network, phylogeny, polynomial, Program ARTNET, Program CMPT, reconstruction.
Note: http://grid.cs.gsu.edu/~xguo9/publications/2013_Cloud%20computing%20for%20de%20novo%20metagenomic%20sequence%20assembly.pdf#page=123.

Toggle abstract

@InProceedings{VCHLSSY,
AUTHOR = {Vu, Hoa and Chin, Francis and Hon, Wing-Kai and Leung, Henry and Sadakane, Kunihiko and Sung, Wing-Kin and Yiu, Siu-Ming},
TITLE = {Reconstructing k-Reticulated Phylogenetic Network from a Set of Gene Trees},
YEAR = {2013},
BOOKTITLE = {ISBRA13},
VOLUME = {7875},
PAGES = {112-124},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-642-38036-5_14},
NOTE = {http://grid.cs.gsu.edu/~xguo9/publications/2013_Cloud%20computing%20for%20de%20novo%20metagenomic%20sequence%20assembly.pdf#page=123},
KEYWORDS = {from rooted trees, k-reticulated, phylogenetic network, phylogeny, polynomial, Program ARTNET, Program CMPT, reconstruction}
}

15

Mukul S. Bansal, Guy Banay, Timothy J. Harlow, J. Peter Gogarten and Ron Shamir. Systematic inference of highways of horizontal gene transfer in prokaryotes. In BIO, Vol. 29(5):571-579, 2013.
Keywords: duplication, explicit network, from species tree, from unrooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program HiDe, Program RANGER-DTL, reconstruction.
Note: http://people.csail.mit.edu/mukul/Bansal_Highways_Bioinformatics_2013.pdf.

@Article{BBHGS2013,
AUTHOR = {Bansal, Mukul S. and Banay, Guy and Harlow, Timothy J. and Gogarten, J. Peter and Shamir, Ron},
TITLE = {Systematic inference of highways of horizontal gene transfer in prokaryotes},
YEAR = {2013},
JOURNAL = {BIO},
VOLUME = {29},
NUMBER = {5},
PAGES = {571-579},
URL = {http://dx.doi.org/10.1093/bioinformatics/btt021},
NOTE = {http://people.csail.mit.edu/mukul/Bansal_Highways_Bioinformatics_2013.pdf},
KEYWORDS = {duplication, explicit network, from species tree, from unrooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program HiDe, Program RANGER-DTL, reconstruction}
}

16

Simone Linz, Katherine St. John and Charles Semple. Counting trees in a phylogenetic network is #P-complete. In SICOMP, Vol. 42(4):1768-1776, 2013.
Keywords: counting, from network, phylogenetic network, phylogeny.
Note: http://ab.inf.uni-tuebingen.de/people/linz/publications/counting.pdf.

@Article{LSS2013,
AUTHOR = {Linz, Simone and St. John, Katherine and Semple, Charles},
TITLE = {Counting trees in a phylogenetic network is #P-complete},
YEAR = {2013},
JOURNAL = {SICOMP},
VOLUME = {42},
NUMBER = {4},
PAGES = {1768-1776},
URL = {http://dx.doi.org/10.1137/12089394x},
NOTE = {http://ab.inf.uni-tuebingen.de/people/linz/publications/counting.pdf},
KEYWORDS = {counting, from network, phylogenetic network, phylogeny}
}

17

Eric Bapteste, Leo van Iersel, Axel Janke, Scott Kelchner, Steven Kelk, James O. McInerney, David A. Morrison, Luay Nakhleh, Mike Steel, Leen Stougie and James B. Whitfield. Networks: expanding evolutionary thinking. In Trends in Genetics, Vol. 29(8):439-441, 2013.
Keywords: abstract network, explicit network, phylogenetic network, phylogeny, reconstruction.
Note: http://bioinf.nuim.ie/wp-content/uploads/2013/06/Bapteste-TiG-2013.pdf.

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@Article{BIJKKMMNSSW2013,
AUTHOR = {Bapteste, Eric and van Iersel, Leo and Janke, Axel and Kelchner, Scott and Kelk, Steven and McInerney, James O. and Morrison, David A. and Nakhleh, Luay and Steel, Mike and Stougie, Leen and Whitfield, James B.},
TITLE = {Networks: expanding evolutionary thinking},
YEAR = {2013},
JOURNAL = {Trends in Genetics},
VOLUME = {29},
NUMBER = {8},
PAGES = {439-441},
URL = {http://dx.doi.org/10.1016/j.tig.2013.05.007},
NOTE = {http://bioinf.nuim.ie/wp-content/uploads/2013/06/Bapteste-TiG-2013.pdf},
KEYWORDS = {abstract network, explicit network, phylogenetic network, phylogeny, reconstruction}
}

18

Yun Yu, R. Matthew Barnett and Luay Nakhleh. Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting. In Systematic Biology, Vol. 62(5):738-751, 2013.
Keywords: from network, from rooted trees, hybridization, lineage sorting, parsimony, phylogenetic network, phylogeny, Program PhyloNet, reconstruction.

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@Article{YBN2013,
AUTHOR = {Yu, Yun and Barnett, R. Matthew and Nakhleh, Luay},
TITLE = {Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting},
YEAR = {2013},
JOURNAL = {Systematic Biology},
VOLUME = {62},
NUMBER = {5},
PAGES = {738-751},
URL = {http://dx.doi.org/10.1093/sysbio/syt037},
KEYWORDS = {from network, from rooted trees, hybridization, lineage sorting, parsimony, phylogenetic network, phylogeny, Program PhyloNet, reconstruction}
}

19

Juan Wang, Maozu Guo, Xiaoyan Liu, Yang Liu, Chunyu Wang, Linlin Xing and Kai Che. LNETWORK: An Efficient and Effective Method for Constructing Phylogenetic Networks. In BIO, Vol. 29(18):2269-2276, 2013.
Keywords: explicit network, from rooted trees, phylogenetic network, phylogeny, Program LNetwork, reconstruction, software.

Toggle abstract

@Article{WGLLWXC2013,
AUTHOR = {Wang, Juan and Guo, Maozu and Liu, Xiaoyan and Liu, Yang and Wang, Chunyu and Xing, Linlin and Che, Kai},
TITLE = {LNETWORK: An Efficient and Effective Method for Constructing Phylogenetic Networks},
YEAR = {2013},
JOURNAL = {BIO},
VOLUME = {29},
NUMBER = {18},
PAGES = {2269-2276},
URL = {http://dx.doi.org/10.1093/bioinformatics/btt378},
KEYWORDS = {explicit network, from rooted trees, phylogenetic network, phylogeny, Program LNetwork, reconstruction, software}
}

20

Juan Wang, Maozu Guo, Linlin Xing, Kai Che, Xiaoyan Liu and Chunyu Wang. BIMLR: A Method for Constructing Rooted Phylogenetic Networks from Rooted Phylogenetic Trees. In Gene, Vol. 527(1):344-351, 2013.
Keywords: explicit network, from clusters, from rooted trees, phylogenetic network, phylogeny, Program BIMLR, Program Dendroscope, reconstruction, software.

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@Article{WGXCLW2013b,
AUTHOR = {Wang, Juan and Guo, Maozu and Xing, Linlin and Che, Kai and Liu, Xiaoyan and Wang, Chunyu},
TITLE = {BIMLR: A Method for Constructing Rooted Phylogenetic Networks from Rooted Phylogenetic Trees},
YEAR = {2013},
JOURNAL = {Gene},
VOLUME = {527},
NUMBER = {1},
PAGES = {344-351},
URL = {http://dx.doi.org/10.1016/j.gene.2013.06.036},
KEYWORDS = {explicit network, from clusters, from rooted trees, phylogenetic network, phylogeny, Program BIMLR, Program Dendroscope, reconstruction, software}
}

21

Zhi-Zhong Chen and Lusheng Wang. An Ultrafast Tool for Minimum Reticulate Networks. In JCB, Vol. 20(1):38-41, 2013.
Keywords: agreement forest, explicit network, from rooted trees, phylogenetic network, phylogeny, Program ultra-Net, reconstruction.
Note: http://www.cs.cityu.edu.hk/~lwang/research/jcb2013.pdf.

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@Article{ChenWang2013,
AUTHOR = {Chen, Zhi-Zhong and Wang, Lusheng},
TITLE = {An Ultrafast Tool for Minimum Reticulate Networks},
YEAR = {2013},
JOURNAL = {JCB},
VOLUME = {20},
NUMBER = {1},
PAGES = {38-41},
URL = {http://dx.doi.org/10.1089/cmb.2012.0240},
NOTE = {http://www.cs.cityu.edu.hk/~lwang/research/jcb2013.pdf},
KEYWORDS = {agreement forest, explicit network, from rooted trees, phylogenetic network, phylogeny, Program ultra-Net, reconstruction}
}

22

Simone Linz. Reticulation. In Brenner's Encyclopedia of Genetics (Second Edition), 2013.
Keywords: phylogenetic network, phylogeny, survey.

@InBook{Linz2013,
AUTHOR = {Linz, Simone},
TITLE = {Reticulation},
YEAR = {2013},
BOOKTITLE = {Brenner's Encyclopedia of Genetics (Second Edition)},
URL = {http://dx.doi.org/10.1016/B978-0-12-374984-0.01317-6},
KEYWORDS = {phylogenetic network, phylogeny, survey}
}

23

Peter J. Humphries, Simone Linz and Charles Semple. Cherry picking: a characterization of the temporal hybridization number for a set of phylogenies. In BMB, Vol. 75(10):1879-1890, 2013.
Keywords: characterization, cherry-picking, from rooted trees, hybridization, NP complete, phylogenetic network, phylogeny, reconstruction, time consistent network.
Note: http://ab.inf.uni-tuebingen.de/people/linz/publications/CPSpaper.pdf.

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@Article{HLS2013b,
AUTHOR = {Humphries, Peter J. and Linz, Simone and Semple, Charles},
TITLE = {Cherry picking: a characterization of the temporal hybridization number for a set of phylogenies},
YEAR = {2013},
JOURNAL = {BMB},
VOLUME = {75},
NUMBER = {10},
PAGES = {1879-1890},
URL = {http://dx.doi.org/10.1007/s11538-013-9874-x},
NOTE = {http://ab.inf.uni-tuebingen.de/people/linz/publications/CPSpaper.pdf},
KEYWORDS = {characterization, cherry-picking, from rooted trees, hybridization, NP complete, phylogenetic network, phylogeny, reconstruction, time consistent network}
}

24

Willem Sonke. Reconstructing a level-1-network from quartets. 2013.
Keywords: abstract network, from quartets, phylogenetic network, phylogeny, polynomial, Program Fylogenetica, reconstruction, software, visualization.
Note: http://alexandria.tue.nl/extra1/afstversl/wsk-i/sonke2013.pdf.

@Misc{Sonke2013,
AUTHOR = {Sonke, Willem},
TITLE = {Reconstructing a level-1-network from quartets},
YEAR = {2013},
NOTE = {http://alexandria.tue.nl/extra1/afstversl/wsk-i/sonke2013.pdf},
KEYWORDS = {abstract network, from quartets, phylogenetic network, phylogeny, polynomial, Program Fylogenetica, reconstruction, software, visualization}
}

25

Sha Zhu. Stochastic tree models and probabilistic modelling of gene trees of given species networks. PhD thesis, University of Canterbury, New Zealand, 2013.
Keywords: from network, generation, phylogenetic network, phylogeny, simulation, statistical model.
Note: http://hdl.handle.net/10092/7944.

@PhdThesis{Zhu2013,
AUTHOR = {Zhu, Sha},
TITLE = {Stochastic tree models and probabilistic modelling of gene trees of given species networks},
YEAR = {2013},
SCHOOL = {University of Canterbury, New Zealand},
NOTE = {http://hdl.handle.net/10092/7944},
KEYWORDS = {from network, generation, phylogenetic network, phylogeny, simulation, statistical model}
}

26

Alexey A. Morozov, Yuri P. Galachyants and Yelena V. Likhoshway. Inferring Phylogenetic Networks from Gene Order Data. In BMRI, Vol. 2013(503193):1-7, 2013.
Keywords: abstract network, from distances, from gene order, NeighborNet, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split decomposition, split network.

Toggle abstract

@Article{MGL2013,
AUTHOR = {Morozov, Alexey A. and Galachyants, Yuri P. and Likhoshway, Yelena V.},
TITLE = {Inferring Phylogenetic Networks from Gene Order Data},
YEAR = {2013},
JOURNAL = {BMRI},
VOLUME = {2013},
NUMBER = {503193},
PAGES = {1-7},
URL = {http://dx.doi.org/10.1155/2013/503193},
KEYWORDS = {abstract network, from distances, from gene order, NeighborNet, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split decomposition, split network}
}

27

Celine Scornavacca, Paprotny Wojciech, Vincent Berry and Vincent Ranwez. Representing a set of reconciliations in a compact way. In JBCB, Vol. 11(2):1250025, 2013.
Keywords: duplication, explicit network, from network, from rooted trees, from species tree, phylogeny, Program GraphDTL, Program TERA, visualization.
Note: http://hal-lirmm.ccsd.cnrs.fr/lirmm-00818801.

Toggle abstract

@Article{SPBR2013,
AUTHOR = {Scornavacca, Celine and Wojciech, Paprotny and Berry, Vincent and Ranwez, Vincent},
TITLE = {Representing a set of reconciliations in a compact way},
YEAR = {2013},
JOURNAL = {JBCB},
VOLUME = {11},
NUMBER = {2},
PAGES = {1250025},
URL = {http://dx.doi.org/10.1142/S0219720012500254},
NOTE = {http://hal-lirmm.ccsd.cnrs.fr/lirmm-00818801},
KEYWORDS = {duplication, explicit network, from network, from rooted trees, from species tree, phylogeny, Program GraphDTL, Program TERA, visualization}
}

28

Thi-Hau Nguyen. Réconciliations: corriger des arbres de gènes et inférer la fiabilité des événements évolutifs. PhD thesis, Université Montpellier 2, France, 2013.
Keywords: duplication, explicit network, from rooted trees, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program Mowgli, Program MowgliNNI, reconstruction.
Note: http://www.biu-montpellier.fr/florabium/servlet/DocumentFileManager?source=ged&document=ged:IDOCS:247665&resolution=&recordId=theses%3ABIU_THESE%3A1789&file=.

@PhdThesis{Nguyen2013,
AUTHOR = {Nguyen, Thi-Hau},
TITLE = {R{\~A}�conciliations: corriger des arbres de g{\~A}�nes et inf{\~A}�rer la fiabilit{\~A}� des {\~A}�v{\~A}�nements {\~A}�volutifs},
YEAR = {2013},
SCHOOL = {Universit{\~A}� Montpellier 2, France},
NOTE = {http://www.biu-montpellier.fr/florabium/servlet/DocumentFileManager?source=ged{\&}document=ged:IDOCS:247665{\&}resolution={\&}recordId=theses%3ABIU_THESE%3A1789{\&}file=},
KEYWORDS = {duplication, explicit network, from rooted trees, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program Mowgli, Program MowgliNNI, reconstruction}
}

29

Luay Nakhleh. Computational approaches to species phylogeny inference and gene tree reconciliation. In Trends in Ecology and Evolution, Vol. 28(12):719-728, 2013.
Keywords: from rooted trees, from species tree, phylogenetic network, phylogeny, reconstruction, survey.
Note: http://bioinfo.cs.rice.edu/sites/bioinfo.cs.rice.edu/files/TREE-Nakhleh13.pdf.

Toggle abstract

@Article{Nakhleh2013,
AUTHOR = {Nakhleh, Luay},
TITLE = {Computational approaches to species phylogeny inference and gene tree reconciliation},
YEAR = {2013},
JOURNAL = {Trends in Ecology and Evolution},
VOLUME = {28},
NUMBER = {12},
PAGES = {719-728},
URL = {http://dx.doi.org/10.1016/j.tree.2013.09.004},
NOTE = {http://bioinfo.cs.rice.edu/sites/bioinfo.cs.rice.edu/files/TREE-Nakhleh13.pdf},
KEYWORDS = {from rooted trees, from species tree, phylogenetic network, phylogeny, reconstruction, survey}
}

30

Thi-Hau Nguyen, Vincent Ranwez, Vincent Berry and Celine Scornavacca. Support Measures to Estimate the Reliability of Evolutionary Events Predicted by Reconciliation Methods. In PLoS ONE, Vol. 8(10):e73667, 2013.
Keywords: duplication, from rooted trees, from species tree, phylogenetic network, phylogeny, polynomial, Program GraphDTL, reconstruction.
Note: http://dx.doi.org/10.1371/journal.pone.0073667.

Toggle abstract

@Article{NRBS2013,
AUTHOR = {Nguyen, Thi-Hau and Ranwez, Vincent and Berry, Vincent and Scornavacca, Celine},
TITLE = {Support Measures to Estimate the Reliability of Evolutionary Events Predicted by Reconciliation Methods},
YEAR = {2013},
JOURNAL = {PLoS ONE},
VOLUME = {8},
NUMBER = {10},
PAGES = {e73667},
URL = {http://dx.doi.org/10.1371/journal.pone.0073667},
NOTE = {http://dx.doi.org/10.1371/journal.pone.0073667},
KEYWORDS = {duplication, from rooted trees, from species tree, phylogenetic network, phylogeny, polynomial, Program GraphDTL, reconstruction}
}

31

Mukul S. Bansal, Eric J. Alm and Manolis Kellis. Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss. In JCB, Vol. 20(10):738-754, 2013.
Keywords: duplication, from rooted trees, from species tree, loss, phylogenetic network, phylogeny, Program RANGER-DTL, reconstruction.
Note: http://www.engr.uconn.edu/~mukul/Bansal_JCB2013.pdf.

Toggle abstract

@Article{BAK2013b,
AUTHOR = {Bansal, Mukul S. and Alm, Eric J. and Kellis, Manolis},
TITLE = {Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss},
YEAR = {2013},
JOURNAL = {JCB},
VOLUME = {20},
NUMBER = {10},
PAGES = {738-754},
URL = {http://dx.doi.org/10.1089/cmb.2013.0073},
NOTE = {http://www.engr.uconn.edu/~mukul/Bansal_JCB2013.pdf},
KEYWORDS = {duplication, from rooted trees, from species tree, loss, phylogenetic network, phylogeny, Program RANGER-DTL, reconstruction}
}

32

David A. Morrison. Phylogenetic networks are fundamentally different from other kinds of biological networks. In WenJun Zhang editor, Network Biology: Theories, Methods and Applications, Chapter 2, Nova Publishers, 2013.
Keywords: abstract network, explicit network, phylogenetic network, phylogeny.

@InBook{Morrison2013,
AUTHOR = {Morrison, David A.},
TITLE = {Phylogenetic networks are fundamentally different from other kinds of biological networks},
YEAR = {2013},
BOOKTITLE = {Network Biology: Theories, Methods and Applications},
EDITOR = {Zhang, WenJun},
PUBLISHER = {Nova Publishers},
CHAPTER = {2},
KEYWORDS = {abstract network, explicit network, phylogenetic network, phylogeny}
}

33

Steven Kelk, Simone Linz and David A. Morrison. Fighting network space: it is time for an SQL-type language to filter phylogenetic networks. 2013.
Keywords: database, explicit network, from network, phylogenetic network, phylogeny.
Note: http://arxiv.org/abs/1310.6844.

@Misc{KLM2013,
AUTHOR = {Kelk, Steven and Linz, Simone and Morrison, David A.},
TITLE = {Fighting network space: it is time for an SQL-type language to filter phylogenetic networks},
YEAR = {2013},
NOTE = {http://arxiv.org/abs/1310.6844},
KEYWORDS = {database, explicit network, from network, phylogenetic network, phylogeny}
}

34

Leo van Iersel, Steven Kelk, Nela Lekic and Leen Stougie. A short note on exponential-time algorithms for hybridization number. 2013.
Keywords: explicit network, exponential algorithm, from rooted trees, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1312.1255.

@Misc{IKLS2013,
AUTHOR = {van Iersel, Leo and Kelk, Steven and Lekic, Nela and Stougie, Leen},
TITLE = {A short note on exponential-time algorithms for hybridization number},
YEAR = {2013},
NOTE = {http://arxiv.org/abs/1312.1255},
KEYWORDS = {explicit network, exponential algorithm, from rooted trees, phylogenetic network, phylogeny, reconstruction}
}

35

Yun Yu, Nikola Ristic and Luay Nakhleh. Fast algorithms and heuristics for phylogenomics under ILS and hybridization. In RECOMB-CG'13, Vol. 14(Suppl 15):S6 of BMCB, 2013.
Keywords: from network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program PhyloNet, reconstruction.

@InProceedings{YRN2013,
AUTHOR = {Yu, Yun and Ristic, Nikola and Nakhleh, Luay},
TITLE = {Fast algorithms and heuristics for phylogenomics under ILS and hybridization},
YEAR = {2013},
BOOKTITLE = {RECOMB-CG'13},
VOLUME = {14},
NUMBER = {Suppl 15},
PAGES = {S6},
SERIES = {BMCB},
URL = {http://dx.doi.org/10.1186/1471-2105-14-S15-S6},
KEYWORDS = {from network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program PhyloNet, reconstruction}
}

36

Alberto Apostolico, Matteo Comin, Andreas W. M. Dress and Laxmi Parida. Ultrametric networks: a new tool for phylogenetic analysis. In Algorithms for Molecular Biology, Vol. 8(7):1-10, 2013.
Keywords: abstract network, from distances, phylogenetic network, phylogeny, Program Ultranet.
Note: http://dx.doi.org/10.1186/1748-7188-8-7.

Toggle abstract

@Article{ACDP2013,
AUTHOR = {Apostolico, Alberto and Comin, Matteo and Dress, Andreas W. M. and Parida, Laxmi},
TITLE = {Ultrametric networks: a new tool for phylogenetic analysis},
YEAR = {2013},
JOURNAL = {Algorithms for Molecular Biology},
VOLUME = {8},
NUMBER = {7},
PAGES = {1-10},
URL = {http://dx.doi.org/10.1186/1748-7188-8-7},
NOTE = {http://dx.doi.org/10.1186/1748-7188-8-7},
KEYWORDS = {abstract network, from distances, phylogenetic network, phylogeny, Program Ultranet}
}

37

Mehdi Layeghifard, Pedro R. Peres-Neto and Vladimir Makarenkov. Inferring explicit weighted consensus networks to represent alternative evolutionary histories. In BMCEB, Vol. 13(274):1-25, 2013.
Keywords: explicit network, from rooted trees, from species tree, phylogenetic network, phylogeny, Program ConsensusNetwork, reconstruction.
Note: http://dx.doi.org/10.1186/1471-2148-13-274.

Toggle abstract

@Article{LPM2013,
AUTHOR = {Layeghifard, Mehdi and Peres-Neto, Pedro R. and Makarenkov, Vladimir},
TITLE = {Inferring explicit weighted consensus networks to represent alternative evolutionary histories},
YEAR = {2013},
JOURNAL = {BMCEB},
VOLUME = {13},
NUMBER = {274},
PAGES = {1-25},
URL = {http://dx.doi.org/10.1186/1471-2148-13-274},
NOTE = {http://dx.doi.org/10.1186/1471-2148-13-274},
KEYWORDS = {explicit network, from rooted trees, from species tree, phylogenetic network, phylogeny, Program ConsensusNetwork, reconstruction}
}

38

Gergely J. Szöllösi, Eric Tannier, Nicolas Lartillot and Vincent Daubin. Lateral Gene Transfer from the Dead. In Systematic Biology, Vol. 62(3):386-397, 2013.
Keywords: duplication, lateral gene transfer, likelihood, loss, phylogeny, Program TERA, reconstruction.
Note: http://dx.doi.org/10.1093/sysbio/syt003.

Toggle abstract

@Article{STLD2013,
AUTHOR = {Sz{\~A}�ll{\~A}�si, Gergely J. and Tannier, Eric and Lartillot, Nicolas and Daubin, Vincent},
TITLE = {Lateral Gene Transfer from the Dead},
YEAR = {2013},
JOURNAL = {Systematic Biology},
VOLUME = {62},
NUMBER = {3},
PAGES = {386-397},
URL = {http://dx.doi.org/10.1093/sysbio/syt003},
NOTE = {http://dx.doi.org/10.1093/sysbio/syt003},
KEYWORDS = {duplication, lateral gene transfer, likelihood, loss, phylogeny, Program TERA, reconstruction}
}

39

Gergely J. Szöllösi, Wojciech Rosikiewicz, Bastien Boussau, Eric Tannier and Vincent Daubin. Efficient Exploration of the Space of Reconciled Gene Trees. In Systematic Biology, Vol. 62(6):901-912, 2013.
Keywords: duplication, explicit network, lateral gene transfer, likelihood, loss, phylogeny, Program ALE, reconstruction.
Note: http://arxiv.org/abs/1306.2167.

Toggle abstract

@Article{SRBTD2013,
AUTHOR = {Sz{\~A}�ll{\~A}�si, Gergely J. and Rosikiewicz, Wojciech and Boussau, Bastien and Tannier, Eric and Daubin, Vincent},
TITLE = {Efficient Exploration of the Space of Reconciled Gene Trees},
YEAR = {2013},
JOURNAL = {Systematic Biology},
VOLUME = {62},
NUMBER = {6},
PAGES = {901-912},
URL = {http://dx.doi.org/10.1093/sysbio/syt054},
NOTE = {http://arxiv.org/abs/1306.2167},
KEYWORDS = {duplication, explicit network, lateral gene transfer, likelihood, loss, phylogeny, Program ALE, reconstruction}
}

40

Zhi-Zhong Chen, Fei Deng and Lusheng Wang. Identifying Duplications and Lateral Gene Transfers Simultaneously and Rapidly. In CIBCB13, Pages 128-135, 2013.
Keywords: duplication, FPT, from rooted trees, from species tree, phylogenetic network, phylogeny, reconstruction.
Note: http://www.cs.cityu.edu.hk/~lwang/research/singaporet2013.pdf.

@InProceedings{CDW2013,
AUTHOR = {Chen, Zhi-Zhong and Deng, Fei and Wang, Lusheng},
TITLE = {Identifying Duplications and Lateral Gene Transfers Simultaneously and Rapidly},
YEAR = {2013},
BOOKTITLE = {CIBCB13},
PAGES = {128-135},
URL = {http://dx.doi.org/10.1109/CIBCB.2013.6595398},
NOTE = {http://www.cs.cityu.edu.hk/~lwang/research/singaporet2013.pdf},
KEYWORDS = {duplication, FPT, from rooted trees, from species tree, phylogenetic network, phylogeny, reconstruction}
}

41

Chris Whidden. Efficient Computation and Application of Maximum Agreement Forests. PhD thesis, Dalhousie University, Canada, 2013.
Keywords: agreement forest, explicit network, FPT, from rooted trees, minimum number, phylogenetic network, phylogeny, reconstruction.
Note: http://hdl.handle.net/10222/35349.

@PhdThesis{Whidden2013,
AUTHOR = {Whidden, Chris},
TITLE = {Efficient Computation and Application of Maximum Agreement Forests},
YEAR = {2013},
SCHOOL = {Dalhousie University, Canada},
URL = {http://hdl.handle.net/10222/35349},
NOTE = {http://hdl.handle.net/10222/35349},
KEYWORDS = {agreement forest, explicit network, FPT, from rooted trees, minimum number, phylogenetic network, phylogeny, reconstruction}
}

42

Yufeng Wu. An Algorithm for Constructing Parsimonious Hybridization Networks with Multiple Phylogenetic Trees. In JCB, Vol. 20(10):792-804, 2013.
Keywords: explicit network, exponential algorithm, from rooted trees, phylogenetic network, phylogeny, Program PIRN, reconstruction.

@Article{Wu2013b,
AUTHOR = {Wu, Yufeng},
TITLE = {An Algorithm for Constructing Parsimonious Hybridization Networks with Multiple Phylogenetic Trees},
YEAR = {2013},
JOURNAL = {JCB},
VOLUME = {20},
NUMBER = {10},
PAGES = {792-804},
URL = {http://dx.doi.org/10.1089/cmb.2013.0072},
KEYWORDS = {explicit network, exponential algorithm, from rooted trees, phylogenetic network, phylogeny, Program PIRN, reconstruction}
}

43

Yao-ban Chan, Vincent Ranwez and Celine Scornavacca. Reconciliation-based detection of co-evolving gene families. In BMC Bioinformatics, Vol. 14(332):1-9, 2013.
Keywords: cophylogeny, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1186/1471-2105-14-332.

@Article{CRS2013,
AUTHOR = {Chan, Yao-ban and Ranwez, Vincent and Scornavacca, Celine},
TITLE = {Reconciliation-based detection of co-evolving gene families},
YEAR = {2013},
JOURNAL = {BMC Bioinformatics},
VOLUME = {14},
NUMBER = {332},
PAGES = {1-9},
URL = {http://dx.doi.org/10.1186/1471-2105-14-332},
NOTE = {http://dx.doi.org/10.1186/1471-2105-14-332},
KEYWORDS = {cophylogeny, phylogeny, reconstruction}
}

44

Sarah Bastkowski. From Trees to Networks and Back. PhD thesis, University of East Anglia, 2013.
Keywords: abstract network, NeighborNet, phylogenetic network, phylogeny, Program FlatNJ, Program QNet, Program SplitsTree, reconstruction, software, split network.
Note: http://spectre-suite-of-phylogenetic-tools-for-reticulate-evolution.readthedocs.io/en/latest/_downloads/spectre_bastkowskis_thesis.pdf.

@PhdThesis{Bastkowski2013,
AUTHOR = {Bastkowski, Sarah},
TITLE = {From Trees to Networks and Back},
YEAR = {2013},
SCHOOL = {University of East Anglia},
NOTE = {http://spectre-suite-of-phylogenetic-tools-for-reticulate-evolution.readthedocs.io/en/latest/_downloads/spectre_bastkowskis_thesis.pdf},
KEYWORDS = {abstract network, NeighborNet, phylogenetic network, phylogeny, Program FlatNJ, Program QNet, Program SplitsTree, reconstruction, software, split network}
}

2012

1

Yun Yu and Luay Nakhleh. Fast Algorithms for Reconciliation under Hybridization and Incomplete Lineage Sorting. 2012.
Keywords: hybridization, lineage sorting, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, software.
Note: http://arxiv.org/abs/1212.1909.

@Misc{YuNakhleh2012,
AUTHOR = {Yu, Yun and Nakhleh, Luay},
TITLE = {Fast Algorithms for Reconciliation under Hybridization and Incomplete Lineage Sorting},
YEAR = {2012},
NOTE = {http://arxiv.org/abs/1212.1909},
KEYWORDS = {hybridization, lineage sorting, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, software}
}

2

Philippe Gambette and Katharina Huber. On Encodings of Phylogenetic Networks of Bounded Level. In JOMB, Vol. 65(1):157-180, 2012.
Keywords: characterization, explicit network, from clusters, from rooted trees, from triplets, galled tree, identifiability, level k phylogenetic network, phylogenetic network, uniqueness, weak hierarchy.
Note: http://hal.archives-ouvertes.fr/hal-00609130/en/.

Toggle abstract

@Article{GambetteHuber2012,
AUTHOR = {Gambette, Philippe and Huber, Katharina},
TITLE = {On Encodings of Phylogenetic Networks of Bounded Level},
YEAR = {2012},
JOURNAL = {JOMB},
VOLUME = {65},
NUMBER = {1},
PAGES = {157-180},
URL = {http://dx.doi.org/10.1007/s00285-011-0456-y},
NOTE = {http://hal.archives-ouvertes.fr/hal-00609130/en/},
KEYWORDS = {characterization, explicit network, from clusters, from rooted trees, from triplets, galled tree, identifiability, level k phylogenetic network, phylogenetic network, uniqueness, weak hierarchy}
}

3

Stephen J. Willson. CSD Homomorphisms Between Phylogenetic Networks. In TCBB, Vol. 9(4), 2012.
Keywords: explicit network, from network, from quartets, phylogenetic network.
Note: http://www.public.iastate.edu/~swillson/Relationships11IEEE.pdf, preliminary version entitled Relationships Among Phylogenetic Networks.

Toggle abstract

@Article{Willson2012,
AUTHOR = {Willson, Stephen J.},
TITLE = {CSD Homomorphisms Between Phylogenetic Networks},
YEAR = {2012},
JOURNAL = {TCBB},
VOLUME = {9},
NUMBER = {4},
URL = {http://dx.doi.org/10.1109/TCBB.2012.52},
NOTE = {http://www.public.iastate.edu/~swillson/Relationships11IEEE.pdf, preliminary version entitled Relationships Among Phylogenetic Networks},
KEYWORDS = {explicit network, from network, from quartets, phylogenetic network}
}

4

Steven Kelk, Celine Scornavacca and Leo van Iersel. On the elusiveness of clusters. In TCBB, Vol. 9(2):517-534, 2012.
Keywords: explicit network, from clusters, from rooted trees, from triplets, level k phylogenetic network, phylogenetic network, phylogeny, Program Clustistic, reconstruction, software.
Note: http://arxiv.org/abs/1103.1834.

@Article{KSI2012,
AUTHOR = {Kelk, Steven and Scornavacca, Celine and van Iersel, Leo},
TITLE = {On the elusiveness of clusters},
YEAR = {2012},
JOURNAL = {TCBB},
VOLUME = {9},
NUMBER = {2},
PAGES = {517-534},
URL = {http://dx.doi.org/10.1109/tcbb.2011.128},
NOTE = {http://arxiv.org/abs/1103.1834},
KEYWORDS = {explicit network, from clusters, from rooted trees, from triplets, level k phylogenetic network, phylogenetic network, phylogeny, Program Clustistic, reconstruction, software}
}

5

Hadi Poormohammadi and Changiz Eslahchi. Constructing Rooted Phylogenetic Networks from Triplets based on Height Function. In International Journal of Emerging Technology and Advanced Engineering, Vol. 2(7):389-393, 2012.
Keywords: from triplets, heuristic, phylogenetic network, phylogeny, reconstruction.
Note: http://www.ijetae.com/files/Volume2Issue7/IJETAE_0712_67.pdf.

@Article{PoormohammadiEslahchi2012,
AUTHOR = {Poormohammadi, Hadi and Eslahchi, Changiz},
TITLE = {Constructing Rooted Phylogenetic Networks from Triplets based on Height Function},
YEAR = {2012},
JOURNAL = {International Journal of Emerging Technology and Advanced Engineering},
VOLUME = {2},
NUMBER = {7},
PAGES = {389-393},
URL = {http://www.ijetae.com/files/Volume2Issue7/IJETAE_0712_67.pdf},
NOTE = {http://www.ijetae.com/files/Volume2Issue7/IJETAE_0712_67.pdf},
KEYWORDS = {from triplets, heuristic, phylogenetic network, phylogeny, reconstruction}
}

6

Jeremy G. Sumner, Barbara R. Holland and Peter D. Jarvis. The algebra of the general Markov model on phylogenetic trees and networks. In BMB, Vol. 74(4):858-880, 2012.
Keywords: abstract network, phylogenetic network, phylogeny, split, split network, statistical model.
Note: http://arxiv.org/abs/1012.5165.

Toggle abstract

@Article{SHJ2012,
AUTHOR = {Sumner, Jeremy G. and Holland, Barbara R. and Jarvis, Peter D.},
TITLE = {The algebra of the general Markov model on phylogenetic trees and networks},
YEAR = {2012},
JOURNAL = {BMB},
VOLUME = {74},
NUMBER = {4},
PAGES = {858-880},
URL = {http://dx.doi.org/10.1007/s11538-011-9691-z},
NOTE = {http://arxiv.org/abs/1012.5165},
KEYWORDS = {abstract network, phylogenetic network, phylogeny, split, split network, statistical model}
}

7

Andreas W. M. Dress, Katharina Huber, Jacobus Koolen, Andreas Spillner and Vincent Moulton. An Introduction to Phylogenetic Combinatorics. Cambridge University Press, 2012.
Keywords: phylogenetic network, split network, survey.
Note: http://www.amazon.fr/Basic-Phylogenetic-Combinatorics-Andreas-Dress/dp/0521768322.

@Book{DHKSM2012,
AUTHOR = {Dress, Andreas W. M. and Huber, Katharina and Koolen, Jacobus and Spillner, Andreas and Moulton, Vincent},
TITLE = {An Introduction to Phylogenetic Combinatorics},
YEAR = {2012},
PUBLISHER = {Cambridge University Press},
NOTE = {http://www.amazon.fr/Basic-Phylogenetic-Combinatorics-Andreas-Dress/dp/0521768322},
KEYWORDS = {phylogenetic network, split network, survey}
}

8

Andreas Spillner, Binh T. Nguyen and Vincent Moulton. Constructing and Drawing Regular Planar Split Networks. In TCBB, Vol. 9(2):395-407, 2012.
Keywords: abstract network, from splits, phylogenetic network, phylogeny, reconstruction, visualization.
Note: slides and presentation available at http://www.newton.ac.uk/programmes/PLG/seminars/062111501.html.

Toggle abstract

@Article{SNM2012,
AUTHOR = {Spillner, Andreas and Nguyen, Binh T. and Moulton, Vincent},
TITLE = {Constructing and Drawing Regular Planar Split Networks},
YEAR = {2012},
JOURNAL = {TCBB},
VOLUME = {9},
NUMBER = {2},
PAGES = {395-407},
URL = {http://dx.doi.org/10.1109/TCBB.2011.115},
NOTE = {slides and presentation available at http://www.newton.ac.uk/programmes/PLG/seminars/062111501.html},
KEYWORDS = {abstract network, from splits, phylogenetic network, phylogeny, reconstruction, visualization}
}

9

Paul Phipps and Sergey Bereg. Optimizing Phylogenetic Networks for Circular Split Systems. In TCBB, Vol. 9(2):535-547, 2012.
Keywords: abstract network, from distances, from splits, phylogenetic network, phylogeny, Program PhippsNetwork, reconstruction, software.

Toggle abstract

@Article{PhippsBereg2012,
AUTHOR = {Phipps, Paul and Bereg, Sergey},
TITLE = {Optimizing Phylogenetic Networks for Circular Split Systems},
YEAR = {2012},
JOURNAL = {TCBB},
VOLUME = {9},
NUMBER = {2},
PAGES = {535-547},
URL = {http://dx.doi.org//10.1109/TCBB.2011.109},
KEYWORDS = {abstract network, from distances, from splits, phylogenetic network, phylogeny, Program PhippsNetwork, reconstruction, software}
}

10

Andreas Spillner and Vincent Moulton. Optimal algorithms for computing edge weights in planar split-networks. In Journal of Applied Mathematics and Computing, Vol. 39(1-2):1-13, 2012.
Keywords: abstract network, from distances, phylogenetic network, phylogeny, reconstruction, split, split network.
Note: http://dx.doi.org/10.1007/s12190-011-0506-z.

Toggle abstract

@Article{MoultonSpillner2012,
AUTHOR = {Spillner, Andreas and Moulton, Vincent},
TITLE = {Optimal algorithms for computing edge weights in planar split-networks},
YEAR = {2012},
JOURNAL = {Journal of Applied Mathematics and Computing},
VOLUME = {39},
NUMBER = {1-2},
PAGES = {1-13},
URL = {http://dx.doi.org/10.1007/s12190-011-0506-z},
NOTE = {http://dx.doi.org/10.1007/s12190-011-0506-z},
KEYWORDS = {abstract network, from distances, phylogenetic network, phylogeny, reconstruction, split, split network}
}

11

Magnus Bordewich and Charles Semple. Budgeted Nature Reserve Selection with diversity feature loss and arbitrary split systems. In JOMB, Vol. 64(1):69-85, 2012.
Keywords: abstract network, approximation, diversity, phylogenetic network, polynomial, split network.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BS11.pdf.

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@Article{BordewichSemple2012,
AUTHOR = {Bordewich, Magnus and Semple, Charles},
TITLE = {Budgeted Nature Reserve Selection with diversity feature loss and arbitrary split systems},
YEAR = {2012},
JOURNAL = {JOMB},
VOLUME = {64},
NUMBER = {1},
PAGES = {69-85},
URL = {http://dx.doi.org/10.1007/s00285-011-0405-9},
NOTE = {http://www.math.canterbury.ac.nz/~c.semple/papers/BS11.pdf},
KEYWORDS = {abstract network, approximation, diversity, phylogenetic network, polynomial, split network}
}

12

Celine Scornavacca, Simone Linz and Benjamin Albrecht. A first step towards computing all hybridization networks for two rooted binary phylogenetic trees. In JCB, Vol. 19:1227-1242, 2012.
Keywords: agreement forest, explicit network, FPT, from rooted trees, phylogenetic network, phylogeny, Program Dendroscope, Program Hybroscale, reconstruction.
Note: http://arxiv.org/abs/1109.3268.

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@Article{SLA2012,
AUTHOR = {Scornavacca, Celine and Linz, Simone and Albrecht, Benjamin},
TITLE = {A first step towards computing all hybridization networks for two rooted binary phylogenetic trees},
YEAR = {2012},
JOURNAL = {JCB},
VOLUME = {19},
PAGES = {1227-1242},
URL = {http://dx.doi.org/10.1089/cmb.2012.0192},
NOTE = {http://arxiv.org/abs/1109.3268},
KEYWORDS = {agreement forest, explicit network, FPT, from rooted trees, phylogenetic network, phylogeny, Program Dendroscope, Program Hybroscale, reconstruction}
}

13

Simon Joly. JML: Testing hybridization from species trees. In Molecular Ecology Ressources, Vol. 12(1):179-184, 2012.
Keywords: from species tree, hybridization, lineage sorting, phylogenetic network, phylogeny, Program JML, statistical model.
Note: http://www.plantevolution.org/pdf/JMLpaper_accepted.pdf.

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@Article{Joly2012,
AUTHOR = {Joly, Simon},
TITLE = {JML: Testing hybridization from species trees},
YEAR = {2012},
JOURNAL = {Molecular Ecology Ressources},
VOLUME = {12},
NUMBER = {1},
PAGES = {179-184},
URL = {http://dx.doi.org/10.1111/j.1755-0998.2011.03065.x},
NOTE = {http://www.plantevolution.org/pdf/JMLpaper_accepted.pdf},
KEYWORDS = {from species tree, hybridization, lineage sorting, phylogenetic network, phylogeny, Program JML, statistical model}
}

14

Zhi-Zhong Chen and Lusheng Wang. Algorithms for Reticulate Networks of Multiple Phylogenetic Trees. In TCBB, Vol. 9(2):372-384, 2012.
Keywords: explicit network, from rooted trees, minimum number, phylogenetic network, phylogeny, Program CMPT, Program MaafB, reconstruction, software.
Note: http://rnc.r.dendai.ac.jp/~chen/papers/rMaaf.pdf.

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@Article{CW2012,
AUTHOR = {Chen, Zhi-Zhong and Wang, Lusheng},
TITLE = {Algorithms for Reticulate Networks of Multiple Phylogenetic Trees},
YEAR = {2012},
JOURNAL = {TCBB},
VOLUME = {9},
NUMBER = {2},
PAGES = {372-384},
URL = {http://dx.doi.org/10.1109/TCBB.2011.137},
NOTE = {http://rnc.r.dendai.ac.jp/~chen/papers/rMaaf.pdf},
KEYWORDS = {explicit network, from rooted trees, minimum number, phylogenetic network, phylogeny, Program CMPT, Program MaafB, reconstruction, software}
}

15

Stephen J. Willson. Tree-average distances on certain phylogenetic networks have their weights uniquely determined. In ALMOB, Vol. 7(13), 2012.
Keywords: from distances, from network, normal network, phylogenetic network, phylogeny, reconstruction, tree-child network.
Note: hhttp://www.public.iastate.edu/~swillson/Tree-AverageDis10All.pdf.

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@Article{Willson2012b,
AUTHOR = {Willson, Stephen J.},
TITLE = {Tree-average distances on certain phylogenetic networks have their weights uniquely determined},
YEAR = {2012},
JOURNAL = {ALMOB},
VOLUME = {7},
NUMBER = {13},
URL = {http://dx.doi.org/10.1186/1748-7188-7-13},
NOTE = {hhttp://www.public.iastate.edu/~swillson/Tree-AverageDis10All.pdf},
KEYWORDS = {from distances, from network, normal network, phylogenetic network, phylogeny, reconstruction, tree-child network}
}

16

Changiz Eslahchi, Reza Hassanzadeh, Ehsan Mottaghi, Mahnaz Habibi, Hamid Pezeshk and Mehdi Sadeghi. Constructing circular phylogenetic networks from weighted quartets using simulated annealing. In MBIO, Vol. 235(2):123-127, 2012.
Keywords: abstract network, from quartets, heuristic, phylogenetic network, phylogeny, Program SAQ-Net, Program SplitsTree, reconstruction, simulated annealing, software, split network.
Note: http://dx.doi.org/10.1016/j.mbs.2011.11.003.

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@Article{EHMHPS2012,
AUTHOR = {Eslahchi, Changiz and Hassanzadeh, Reza and Mottaghi, Ehsan and Habibi, Mahnaz and Pezeshk, Hamid and Sadeghi, Mehdi},
TITLE = {Constructing circular phylogenetic networks from weighted quartets using simulated annealing},
YEAR = {2012},
JOURNAL = {MBIO},
VOLUME = {235},
NUMBER = {2},
PAGES = {123-127},
URL = {http://dx.doi.org/10.1016/j.mbs.2011.11.003},
NOTE = {http://dx.doi.org/10.1016/j.mbs.2011.11.003},
KEYWORDS = {abstract network, from quartets, heuristic, phylogenetic network, phylogeny, Program SAQ-Net, Program SplitsTree, reconstruction, simulated annealing, software, split network}
}

17

Benjamin Albrecht, Celine Scornavacca, Alberto Cenci and Daniel H. Huson. Fast computation of minimum hybridization networks. In BIO, Vol. 28(2):191-197, 2012.
Keywords: explicit network, from rooted trees, minimum number, phylogenetic network, phylogeny, Program Dendroscope, Program Hybroscale, reconstruction.
Note: http://dx.doi.org/10.1093/bioinformatics/btr618.

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@Article{ASCH2012,
AUTHOR = {Albrecht, Benjamin and Scornavacca, Celine and Cenci, Alberto and Huson, Daniel H.},
TITLE = {Fast computation of minimum hybridization networks},
YEAR = {2012},
JOURNAL = {BIO},
VOLUME = {28},
NUMBER = {2},
PAGES = {191-197},
URL = {http://dx.doi.org/10.1093/bioinformatics/btr618},
NOTE = {http://dx.doi.org/10.1093/bioinformatics/btr618},
KEYWORDS = {explicit network, from rooted trees, minimum number, phylogenetic network, phylogeny, Program Dendroscope, Program Hybroscale, reconstruction}
}

18

Steven Kelk, Leo van Iersel, Nela Lekic, Simone Linz, Celine Scornavacca and Leen Stougie. Cycle killer... qu'est-ce que c'est? On the comparative approximability of hybridization number and directed feedback vertex set. In SIDMA, Vol. 26(4):1635-1656, 2012.
Keywords: agreement forest, approximation, explicit network, from rooted trees, minimum number, phylogenetic network, phylogeny, Program CycleKiller, reconstruction.
Note: http://arxiv.org/abs/1112.5359, about the title.

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@Article{KILSS2012,
AUTHOR = {Kelk, Steven and van Iersel, Leo and Lekic, Nela and Linz, Simone and Scornavacca, Celine and Stougie, Leen},
TITLE = {Cycle killer... qu'est-ce que c'est? On the comparative approximability of hybridization number and directed feedback vertex set},
YEAR = {2012},
JOURNAL = {SIDMA},
VOLUME = {26},
NUMBER = {4},
PAGES = {1635-1656},
URL = {http://dx.doi.org/10.1137/120864350},
NOTE = {http://arxiv.org/abs/1112.5359, about the title},
KEYWORDS = {agreement forest, approximation, explicit network, from rooted trees, minimum number, phylogenetic network, phylogeny, Program CycleKiller, reconstruction}
}

19

Rosalba Radice. A Bayesian Approach to Modelling Reticulation Events with Application to the Ribosomal Protein Gene rps11 of Flowering Plants. In Australian & New Zealand Journal of Statistics, Vol. 54(4):401-426, 2012.
Keywords: bayesian, phylogenetic network, phylogeny, reconstruction, statistical model.

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@Article{Radice2012,
AUTHOR = {Radice, Rosalba},
TITLE = {A Bayesian Approach to Modelling Reticulation Events with Application to the Ribosomal Protein Gene rps11 of Flowering Plants},
YEAR = {2012},
JOURNAL = {Australian {\&} New Zealand Journal of Statistics},
VOLUME = {54},
NUMBER = {4},
PAGES = {401-426},
URL = {http://dx.doi.org/10.1111/j.1467-842X.2012.00686.x},
KEYWORDS = {bayesian, phylogenetic network, phylogeny, reconstruction, statistical model}
}

20

Philippe Gambette, Vincent Berry and Christophe Paul. Quartets and Unrooted Phylogenetic Networks. In JBCB, Vol. 10(4):1250004, 2012.
Keywords: abstract network, circular split system, explicit network, from quartets, level k phylogenetic network, orientation, phylogenetic network, phylogeny, polynomial, reconstruction, split, split network.
Note: http://hal.archives-ouvertes.fr/hal-00678046/en/.

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@Article{GBP2012,
AUTHOR = {Gambette, Philippe and Berry, Vincent and Paul, Christophe},
TITLE = {Quartets and Unrooted Phylogenetic Networks},
YEAR = {2012},
JOURNAL = {JBCB},
VOLUME = {10},
NUMBER = {4},
PAGES = {1250004},
URL = {http://dx.doi.org/10.1142/S0219720012500047},
NOTE = {http://hal.archives-ouvertes.fr/hal-00678046/en/},
KEYWORDS = {abstract network, circular split system, explicit network, from quartets, level k phylogenetic network, orientation, phylogenetic network, phylogeny, polynomial, reconstruction, split, split network}
}

21

David A. Morrison, Leo van Iersel and Steven Kelk. The Genealogical World of Phylogenetic Networks. Blog, 2012.
Keywords: survey.
Note: http://phylonetworks.blogspot.com/.

@Misc{MLS2012,
AUTHOR = {Morrison, David A. and van Iersel, Leo and Kelk, Steven},
TITLE = {The Genealogical World of Phylogenetic Networks},
YEAR = {2012},
HOWPUBLISHED = {Blog},
URL = {http://phylonetworks.blogspot.com/},
NOTE = {http://phylonetworks.blogspot.com/},
KEYWORDS = {survey}
}

22

Yun Yu, James H. Degnan and Luay Nakhleh. The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection. In PLoS Genetics, Vol. 8(4):e1002660, 2012.
Keywords: AIC, BIC, explicit network, hybridization, phylogenetic network, phylogeny, statistical model.
Note: http://dx.doi.org/10.1371/journal.pgen.1002660.

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@Article{YDN2012,
AUTHOR = {Yu, Yun and Degnan, James H. and Nakhleh, Luay},
TITLE = {The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection},
YEAR = {2012},
JOURNAL = {PLoS Genetics},
VOLUME = {8},
NUMBER = {4},
PAGES = {e1002660},
URL = {http://dx.doi.org/10.1371/journal.pgen.1002660},
NOTE = {http://dx.doi.org/10.1371/journal.pgen.1002660},
KEYWORDS = {AIC, BIC, explicit network, hybridization, phylogenetic network, phylogeny, statistical model}
}

23

Hyun Jung Park and Luay Nakhleh. MURPAR: A fast heuristic for inferring parsimonious phylogenetic networks from multiple gene trees. In ISBRA12, Vol. 7292:213-224 of LNCS, springer, 2012.
Keywords: explicit network, from unrooted trees, heuristic, phylogenetic network, phylogeny, reconstruction, software.
Note: https://www.researchgate.net/profile/Hyun_Jung_Park2/publication/262318595_MURPAR_A_Fast_Heuristic_for_Inferring_Parsimonious_Phylogenetic_Networks_from_Multiple_Gene_Trees/links/54b7e7b50cf269d8cbf58cc4.pdf.

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@InProceedings{ParkNakhleh2012,
AUTHOR = {Park, Hyun Jung and Nakhleh, Luay},
TITLE = {MURPAR: A fast heuristic for inferring parsimonious phylogenetic networks from multiple gene trees},
YEAR = {2012},
BOOKTITLE = {ISBRA12},
VOLUME = {7292},
PAGES = {213-224},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-642-30191-9_20},
NOTE = {https://www.researchgate.net/profile/Hyun_Jung_Park2/publication/262318595_MURPAR_A_Fast_Heuristic_for_Inferring_Parsimonious_Phylogenetic_Networks_from_Multiple_Gene_Trees/links/54b7e7b50cf269d8cbf58cc4.pdf},
KEYWORDS = {explicit network, from unrooted trees, heuristic, phylogenetic network, phylogeny, reconstruction, software}
}

24

Pawel Górecki and Jerzy Tiuryn. Inferring evolutionary scenarios in the duplication, loss and horizontal gene transfer model. In Logic and Program Semantics, Vol. 7230:83-105 of LNCS, springer, 2012.
Keywords: duplication, explicit network, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1007/978-3-642-29485-3_7.

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@InProceedings{GoreckiTiuryn2012,
AUTHOR = {G{\~A}�recki, Pawel and Tiuryn, Jerzy},
TITLE = {Inferring evolutionary scenarios in the duplication, loss and horizontal gene transfer model},
YEAR = {2012},
BOOKTITLE = {Logic and Program Semantics},
VOLUME = {7230},
PAGES = {83-105},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-642-29485-3_7},
NOTE = {http://dx.doi.org/10.1007/978-3-642-29485-3_7},
KEYWORDS = {duplication, explicit network, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction}
}

25

Bonnie Kirkpatrick, Yakir Reshef, Hilary Finucane, Haitao Jiang, Binhai Zhu and Richard M. Karp. Comparing Pedigree Graphs. In JCB, Vol. 19(9):998-1014, 2012.
Keywords: distance between networks, from network, pedigree.
Note: http://arxiv.org/abs/1009.0909, preliminary version as poster at WABI 2010.

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@Article{KRFJZK2012,
AUTHOR = {Kirkpatrick, Bonnie and Reshef, Yakir and Finucane, Hilary and Jiang, Haitao and Zhu, Binhai and Karp, Richard M.},
TITLE = {Comparing Pedigree Graphs},
YEAR = {2012},
JOURNAL = {JCB},
VOLUME = {19},
NUMBER = {9},
PAGES = {998-1014},
URL = {http://dx.doi.org/10.1089/cmb.2011.0254},
NOTE = {http://arxiv.org/abs/1009.0909, preliminary version as poster at WABI 2010},
KEYWORDS = {distance between networks, from network, pedigree}
}

26

Mukul S. Bansal, Eric J. Alm and Manolis Kellis. Efficient Algorithms for the Reconciliation Problem with Gene Duplication, Horizontal Transfer, and Loss. In ISMB12, Vol. 28(12):i283-i291 of BIO, 2012.
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program Angst, Program Mowgli, Program RANGER-DTL, reconstruction.
Note: http://dx.doi.org/10.1093/bioinformatics/bts225.

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@InProceedings{BAK2012,
AUTHOR = {Bansal, Mukul S. and Alm, Eric J. and Kellis, Manolis},
TITLE = {Efficient Algorithms for the Reconciliation Problem with Gene Duplication, Horizontal Transfer, and Loss},
YEAR = {2012},
BOOKTITLE = {ISMB12},
VOLUME = {28},
NUMBER = {12},
PAGES = {i283-i291},
SERIES = {BIO},
URL = {http://dx.doi.org/10.1093/bioinformatics/bts225},
NOTE = {http://dx.doi.org/10.1093/bioinformatics/bts225},
KEYWORDS = {duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program Angst, Program Mowgli, Program RANGER-DTL, reconstruction}
}

27

An-Chiang Chu, Jesper Jansson, Richard Lemence, Alban Mancheron and Kun-Mao Chao. Asymptotic Limits of a New Type of Maximization Recurrence with an Application to Bioinformatics. In TAMC12, Vol. 7287:177-188 of LNCS, springer, 2012.
Keywords: from triplets, galled network, level k phylogenetic network, phylogenetic network.
Note: preliminary version.

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@InProceedings{CJLMC2012,
AUTHOR = {Chu, An-Chiang and Jansson, Jesper and Lemence, Richard and Mancheron, Alban and Chao, Kun-Mao},
TITLE = {Asymptotic Limits of a New Type of Maximization Recurrence with an Application to Bioinformatics},
YEAR = {2012},
BOOKTITLE = {TAMC12},
VOLUME = {7287},
PAGES = {177-188},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-642-29952-0_21},
NOTE = {preliminary version},
KEYWORDS = {from triplets, galled network, level k phylogenetic network, phylogenetic network}
}

28

Reza Hassanzadeh, Changiz Eslahchi and Wing-Kin Sung. Constructing phylogenetic supernetworks based on simulated annealing. In MPE, Vol. 63(3):738-744, 2012.
Keywords: abstract network, from unrooted trees, heuristic, phylogenetic network, phylogeny, Program SNSA, reconstruction, simulated annealing, software, split network.
Note: http://dx.doi.org/10.1016/j.ympev.2012.02.009.

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@Article{HES2012,
AUTHOR = {Hassanzadeh, Reza and Eslahchi, Changiz and Sung, Wing-Kin},
TITLE = {Constructing phylogenetic supernetworks based on simulated annealing},
YEAR = {2012},
JOURNAL = {MPE},
VOLUME = {63},
NUMBER = {3},
PAGES = {738-744},
URL = {http://dx.doi.org/10.1016/j.ympev.2012.02.009},
NOTE = {http://dx.doi.org/10.1016/j.ympev.2012.02.009},
KEYWORDS = {abstract network, from unrooted trees, heuristic, phylogenetic network, phylogeny, Program SNSA, reconstruction, simulated annealing, software, split network}
}

29

Marco Alves, Joãd Alves, Rui Camacho, Pedro Soares and Luísa Pereira. From Networks to Trees. In PACBB'12, Vol. 154:129-136 of Advances in Intelligent and Soft Computing, springer, 2012.
Keywords: from network, phylogenetic network, phylogeny.

@InProceedings{ACSP2012,
AUTHOR = {Alves, Marco and Alves, Jo{\~A}�d and Camacho, Rui and Soares, Pedro and Pereira, Lu{\~A}�sa},
TITLE = {From Networks to Trees},
YEAR = {2012},
BOOKTITLE = {PACBB'12},
VOLUME = {154},
PAGES = {129-136},
SERIES = {Advances in Intelligent and Soft Computing},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-642-28839-5_15},
KEYWORDS = {from network, phylogenetic network, phylogeny}
}

30

Jesper Jansson and Andrzej Lingas. Computing the rooted triplet distance between galled trees by counting triangles. In CPM12, Vol. 7354:385-398 of LNCS, springer, 2012.
Keywords: distance between networks, explicit network, from network, galled tree, phylogenetic network, phylogeny, polynomial, triplet distance.
Note: http://www.df.lth.se/~jj/Publications/d_rt_for_Galled_Trees5_CPM_2012.pdf.

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@InProceedings{JanssonLingas2012,
AUTHOR = {Jansson, Jesper and Lingas, Andrzej},
TITLE = {Computing the rooted triplet distance between galled trees by counting triangles},
YEAR = {2012},
BOOKTITLE = {CPM12},
VOLUME = {7354},
PAGES = {385-398},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-642-31265-6_31},
NOTE = {http://www.df.lth.se/~jj/Publications/d_rt_for_Galled_Trees5_CPM_2012.pdf},
KEYWORDS = {distance between networks, explicit network, from network, galled tree, phylogenetic network, phylogeny, polynomial, triplet distance}
}

31

Tetsuo Asano, Jesper Jansson, Kunihiko Sadakane, Ryuhei Uehara and Gabriel Valiente. Faster computation of the Robinson–Foulds distance between phylogenetic networks. In Information Sciences, Vol. 197:77-90, 2012.
Keywords: distance between networks, explicit network, level k phylogenetic network, phylogenetic network, polynomial, spread.

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@Article{AJSUV2012,
AUTHOR = {Asano, Tetsuo and Jansson, Jesper and Sadakane, Kunihiko and Uehara, Ryuhei and Valiente, Gabriel},
TITLE = {Faster computation of the Robinson{\^a}��Foulds distance between phylogenetic networks},
YEAR = {2012},
JOURNAL = {Information Sciences},
VOLUME = {197},
PAGES = {77-90},
URL = {http://dx.doi.org/10.1016/j.ins.2012.01.038},
KEYWORDS = {distance between networks, explicit network, level k phylogenetic network, phylogenetic network, polynomial, spread}
}

32

Leo van Iersel, Steven Kelk, Nela Lekic and Celine Scornavacca. A practical approximation algorithm for solving massive instances of hybridization number. In WABI12, Vol. 7534(430-440) of LNCS, springer, 2012.
Keywords: agreement forest, approximation, explicit network, from rooted trees, hybridization, phylogenetic network, phylogeny, Program CycleKiller, Program Dendroscope, Program HybridNET, reconstruction, software.
Note: http://arxiv.org/abs/1205.3417.

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@InProceedings{IKLS2012,
AUTHOR = {van Iersel, Leo and Kelk, Steven and Lekic, Nela and Scornavacca, Celine},
TITLE = {A practical approximation algorithm for solving massive instances of hybridization number},
YEAR = {2012},
BOOKTITLE = {WABI12},
VOLUME = {7534},
NUMBER = {430-440},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-642-33122-0_34},
NOTE = {http://arxiv.org/abs/1205.3417},
KEYWORDS = {agreement forest, approximation, explicit network, from rooted trees, hybridization, phylogenetic network, phylogeny, Program CycleKiller, Program Dendroscope, Program HybridNET, reconstruction, software}
}

33

Lavanya Kannan and Ward C Wheeler. Maximum Parsimony on Phylogenetic Networks. In ALMOB, Vol. 7:9, 2012.
Keywords: dynamic programming, explicit network, from sequences, heuristic, parsimony, phylogenetic network, phylogeny.
Note: http://dx.doi.org/10.1186/1748-7188-7-9.

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@Article{KannanWheeler2012,
AUTHOR = {Kannan, Lavanya and Wheeler, Ward C},
TITLE = {Maximum Parsimony on Phylogenetic Networks},
YEAR = {2012},
JOURNAL = {ALMOB},
VOLUME = {7},
PAGES = {9},
URL = {http://dx.doi.org/10.1186/1748-7188-7-9},
NOTE = {http://dx.doi.org/10.1186/1748-7188-7-9},
KEYWORDS = {dynamic programming, explicit network, from sequences, heuristic, parsimony, phylogenetic network, phylogeny}
}

34

Alix Boc, Alpha B. Diallo and Vladimir Makarenkov. T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks. In NAR, Vol. 40(W1):W573-W579, 2012.
Keywords: from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, Program T REX, reconstruction, reticulogram, software.
Note: http://dx.doi.org/10.1093/nar/gks485.

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@Article{BDM2012,
AUTHOR = {Boc, Alix and Diallo, Alpha B. and Makarenkov, Vladimir},
TITLE = {T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks},
YEAR = {2012},
JOURNAL = {NAR},
VOLUME = {40},
NUMBER = {W1},
PAGES = {W573-W579},
URL = {http://dx.doi.org/10.1093/nar/gks485},
NOTE = {http://dx.doi.org/10.1093/nar/gks485},
KEYWORDS = {from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, Program T REX, reconstruction, reticulogram, software}
}

35

Daniel H. Huson and Celine Scornavacca. Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks. In Systematic Biology, Vol. 61(6):1061-1067, 2012.
Keywords: from rooted trees, from triplets, phylogenetic network, phylogeny, Program Dendroscope, reconstruction, software, visualization.

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@Article{HusonScornavacca2012,
AUTHOR = {Huson, Daniel H. and Scornavacca, Celine},
TITLE = {Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks},
YEAR = {2012},
JOURNAL = {Systematic Biology},
VOLUME = {61},
NUMBER = {6},
PAGES = {1061-1067},
URL = {http://dx.doi.org/10.1093/sysbio/sys062},
KEYWORDS = {from rooted trees, from triplets, phylogenetic network, phylogeny, Program Dendroscope, reconstruction, software, visualization}
}

36

Hyun Jung Park and Luay Nakhleh. Inference of reticulate evolutionary histories by maximum likelihood: The performance of information criteria. In RECOMB-CG'12, Vol. 13(suppl 19):S12 of BMCB, 2012.
Keywords: AIC, BIC, explicit network, heuristic, likelihood, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: http://www.biomedcentral.com/1471-2105/13/S19/S12.

@InProceedings{ParkNakhleh2012b,
AUTHOR = {Park, Hyun Jung and Nakhleh, Luay},
TITLE = {Inference of reticulate evolutionary histories by maximum likelihood: The performance of information criteria},
YEAR = {2012},
BOOKTITLE = {RECOMB-CG'12},
VOLUME = {13},
NUMBER = {suppl 19},
PAGES = {S12},
SERIES = {BMCB},
URL = {http://dx.doi.org/10.1186/1471-2105-13-S19-S12},
NOTE = {http://www.biomedcentral.com/1471-2105/13/S19/S12},
KEYWORDS = {AIC, BIC, explicit network, heuristic, likelihood, phylogenetic network, phylogeny, reconstruction, statistical model}
}

37

Zhi-Zhong Chen, Lusheng Wang and Satoshi Yamanaka. A fast tool for minimum hybridization networks. In BMCB, Vol. 13:155, 2012.
Keywords: agreement forest, explicit network, from rooted trees, phylogenetic network, phylogeny, Program FastHN, reconstruction, software.
Note: http://dx.doi.org/10.1186/1471-2105-13-155.

Toggle abstract

@Article{CWY2012,
AUTHOR = {Chen, Zhi-Zhong and Wang, Lusheng and Yamanaka, Satoshi},
TITLE = {A fast tool for minimum hybridization networks},
YEAR = {2012},
JOURNAL = {BMCB},
VOLUME = {13},
PAGES = {155},
URL = {http://dx.doi.org/10.1186/1471-2105-13-155},
NOTE = {http://dx.doi.org/10.1186/1471-2105-13-155},
KEYWORDS = {agreement forest, explicit network, from rooted trees, phylogenetic network, phylogeny, Program FastHN, reconstruction, software}
}

38

Michel Habib and Thu-Hien To. Constructing a Minimum Phylogenetic Network from a Dense Triplet Set. In JBCB, Vol. 10(5):1250013, 2012.
Keywords: explicit network, from triplets, level k phylogenetic network, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://arxiv.org/abs/1103.2266.

Toggle abstract

@Article{HabibTo2012,
AUTHOR = {Habib, Michel and To, Thu-Hien},
TITLE = {Constructing a Minimum Phylogenetic Network from a Dense Triplet Set},
YEAR = {2012},
JOURNAL = {JBCB},
VOLUME = {10},
NUMBER = {5},
PAGES = {1250013},
URL = {http://dx.doi.org/10.1142/S0219720012500138},
NOTE = {http://arxiv.org/abs/1103.2266},
KEYWORDS = {explicit network, from triplets, level k phylogenetic network, phylogenetic network, phylogeny, polynomial, reconstruction}
}

39

Ruogu Sheng and Sergey Bereg. Approximating Metrics with Planar Boundary-Labeled Phylogenetic Networks. In JBCB, Vol. 10(6):1250017, 2012.
Keywords: abstract network, from distances, phylogenetic network, phylogeny, reconstruction.

Toggle abstract

@Article{ShengBereg2012,
AUTHOR = {Sheng, Ruogu and Bereg, Sergey},
TITLE = {Approximating Metrics with Planar Boundary-Labeled Phylogenetic Networks},
YEAR = {2012},
JOURNAL = {JBCB},
VOLUME = {10},
NUMBER = {6},
PAGES = {1250017},
URL = {http://dx.doi.org/10.1142/S0219720012500175},
KEYWORDS = {abstract network, from distances, phylogenetic network, phylogeny, reconstruction}
}

40

Maureen Stolzer, Han Lai, Minli Xu, Deepa Sathaye, Benjamin Vernot and Dannie Durand. Inferring Duplications, Losses, Transfers, and Incomplete Lineage Sorting with Non-Binary Species Trees. In ECCB12, Vol. 28(18):i409-i415 of BIO, 2012.
Keywords: duplication, explicit network, from rooted trees, lateral gene transfer, loss, phylogenetic network, phylogeny, Program Notung, reconstruction.
Note: http://dx.doi.org/10.1093/bioinformatics/bts386.

Toggle abstract

@InProceedings{SLXSVD2012,
AUTHOR = {Stolzer, Maureen and Lai, Han and Xu, Minli and Sathaye, Deepa and Vernot, Benjamin and Durand, Dannie},
TITLE = {Inferring Duplications, Losses, Transfers, and Incomplete Lineage Sorting with Non-Binary Species Trees},
YEAR = {2012},
BOOKTITLE = {ECCB12},
VOLUME = {28},
NUMBER = {18},
PAGES = {i409-i415},
SERIES = {BIO},
URL = {http://dx.doi.org/10.1093/bioinformatics/bts386},
NOTE = {http://dx.doi.org/10.1093/bioinformatics/bts386},
KEYWORDS = {duplication, explicit network, from rooted trees, lateral gene transfer, loss, phylogenetic network, phylogeny, Program Notung, reconstruction}
}

41

Steven Kelk and Celine Scornavacca. Towards the fixed parameter tractability of constructing minimal phylogenetic networks from arbitrary sets of nonbinary trees. 2012.
Keywords: FPT, from rooted trees, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1207.7034.

@Misc{KelkScornavacca2012,
AUTHOR = {Kelk, Steven and Scornavacca, Celine},
TITLE = {Towards the fixed parameter tractability of constructing minimal phylogenetic networks from arbitrary sets of nonbinary trees},
YEAR = {2012},
NOTE = {http://arxiv.org/abs/1207.7034},
KEYWORDS = {FPT, from rooted trees, phylogenetic network, phylogeny, reconstruction}
}

42

Hyun Jung Park. Towards Accurate Reconstruction of Phylogenetic Networks. PhD thesis, Rice University, U.S.A., 2012.
Keywords: explicit network, likelihood, parsimony, phylogenetic network, phylogeny, reconstruction.
Note: http://scholarship.rice.edu/handle/1911/64705.

@PhdThesis{Park2012,
AUTHOR = {Park, Hyun Jung},
TITLE = {Towards Accurate Reconstruction of Phylogenetic Networks},
YEAR = {2012},
SCHOOL = {Rice University, U.S.A.},
URL = {http://scholarship.rice.edu/handle/1911/64705},
NOTE = {http://scholarship.rice.edu/handle/1911/64705},
KEYWORDS = {explicit network, likelihood, parsimony, phylogenetic network, phylogeny, reconstruction}
}

43

Devin Robert Bickner. On normal networks. PhD thesis, Iowa State University, U.S.A., 2012.
Keywords: distance between networks, explicit network, from network, from trees, normal network, phylogenetic network, phylogeny, polynomial, reconstruction, SPR distance.
Note: http://gradworks.umi.com/3511361.pdf.

@PhdThesis{Birckner2012,
AUTHOR = {Bickner, Devin Robert},
TITLE = {On normal networks},
YEAR = {2012},
SCHOOL = {Iowa State University, U.S.A.},
URL = {http://gradworks.umi.com/35/11/3511361.html},
NOTE = {http://gradworks.umi.com/3511361.pdf},
KEYWORDS = {distance between networks, explicit network, from network, from trees, normal network, phylogenetic network, phylogeny, polynomial, reconstruction, SPR distance}
}

44

Thi-Hau Nguyen, Jean-Philippe Doyon, Stéphanie Pointet, Anne-Muriel Chifolleau Arigon, Vincent Ranwez and Vincent Berry. Accounting for Gene Tree Uncertainties Improves Gene Trees and Reconciliation Inference. In WABI12, Vol. 7534:123-134 of LNCS, springer, 2012.
Keywords: duplication, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program Mowgli, reconstruction.
Note: http://hal.archives-ouvertes.fr/hal-00718347/en/.

Toggle abstract

@InProceedings{TDPCRB2012,
AUTHOR = {Nguyen, Thi-Hau and Doyon, Jean-Philippe and Pointet, St{\~A}�phanie and Chifolleau Arigon, Anne-Muriel and Ranwez, Vincent and Berry, Vincent},
TITLE = {Accounting for Gene Tree Uncertainties Improves Gene Trees and Reconciliation Inference},
YEAR = {2012},
BOOKTITLE = {WABI12},
VOLUME = {7534},
PAGES = {123-134},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-642-33122-0_10},
NOTE = {http://hal.archives-ouvertes.fr/hal-00718347/en/},
KEYWORDS = {duplication, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program Mowgli, reconstruction}
}

45

Adrià Alcalà Mena and Francesc Rosselló. Ternary graph isomorphism in polynomial time, after Luks. 2012.
Keywords: distance between networks, explicit network, from network, isomorphism, phylogenetic network, phylogeny, polynomial, Program SAGE.
Note: http://arxiv.org/abs/1209.0871.

@Misc{AlcalaRossello2012,
AUTHOR = {Alcal{\~A}� Mena, Adri{\~A}� and Rossell{\~A}�, Francesc},
TITLE = {Ternary graph isomorphism in polynomial time, after Luks},
YEAR = {2012},
URL = {http://arxiv.org/abs/1209.0871},
NOTE = {http://arxiv.org/abs/1209.0871},
KEYWORDS = {distance between networks, explicit network, from network, isomorphism, phylogenetic network, phylogeny, polynomial, Program SAGE}
}

46

Adrià Alcalà Mena. Trivalent Graph isomorphism in polynomial time. Master's thesis, Universidad de Cantabria, Spain, 2012.
Keywords: distance between networks, explicit network, from network, isomorphism, phylogenetic network, phylogeny, polynomial, Program SAGE.
Note: http://arxiv.org/abs/1209.1040.

@MastersThesis{Alcala2012,
AUTHOR = {Alcal{\~A}� Mena, Adri{\~A}�},
TITLE = {Trivalent Graph isomorphism in polynomial time},
YEAR = {2012},
SCHOOL = {Universidad de Cantabria, Spain},
URL = {http://arxiv.org/abs/1209.1040},
NOTE = {http://arxiv.org/abs/1209.1040},
KEYWORDS = {distance between networks, explicit network, from network, isomorphism, phylogenetic network, phylogeny, polynomial, Program SAGE}
}

47

Joseph K. Pickrell and Jonathan K. Pritchard. Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data. In PLoS Genetics, Vol. 8(11):e1002967, 2012.
Keywords: explicit network, heuristic, likelihood, phylogenetic network, phylogeny, population genetics, Program TreeMix.
Note: http://dx.doi.org/10.1371/journal.pgen.1002967.

Toggle abstract

@Article{PickrellPritchard2012,
AUTHOR = {Pickrell, Joseph K. and Pritchard, Jonathan K.},
TITLE = {Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data},
YEAR = {2012},
JOURNAL = {PLoS Genetics},
VOLUME = {8},
NUMBER = {11},
PAGES = {e1002967},
URL = {http://dx.doi.org/10.1371/journal.pgen.1002967},
NOTE = {http://dx.doi.org/10.1371/journal.pgen.1002967},
KEYWORDS = {explicit network, heuristic, likelihood, phylogenetic network, phylogeny, population genetics, Program TreeMix}
}

48

Nick J. Patterson, Priya Moorjani, Yontao Luo, Swapan Mallick, Nadin Rohland, Yiping Zhan, Teri Genschoreck, Teresa Webster and David Reich. Ancient Admixture in Human History. In Genetics, Vol. 192(3):1065-1093, 2012.
Keywords: explicit network, phylogenetic network, phylogeny, population genetics, Program AdmixTools.
Note: http://genetics.med.harvard.edu/reich/Reich_Lab/Welcome_files/2012_Patterson_AncientAdmixture_Genetics.pdf.

Toggle abstract

@Article{PMLMRZGWR2012,
AUTHOR = {Patterson, Nick J. and Moorjani, Priya and Luo, Yontao and Mallick, Swapan and Rohland, Nadin and Zhan, Yiping and Genschoreck, Teri and Webster, Teresa and Reich, David},
TITLE = {Ancient Admixture in Human History},
YEAR = {2012},
JOURNAL = {Genetics},
VOLUME = {192},
NUMBER = {3},
PAGES = {1065-1093},
URL = {http://dx.doi.org/10.1534/genetics.112.145037},
NOTE = {http://genetics.med.harvard.edu/reich/Reich_Lab/Welcome_files/2012_Patterson_AncientAdmixture_Genetics.pdf},
KEYWORDS = {explicit network, phylogenetic network, phylogeny, population genetics, Program AdmixTools}
}

49

Katharina Huber, Vincent Moulton, Andreas Spillner, Sabine Storandt and Radoslaw Suchecki. Computing a consensus of multilabeled trees. In ALENEX12, Pages 84-92, 2012.
Keywords: duplication, explicit network, exponential algorithm, phylogenetic network, phylogeny.
Note: http://siam.omnibooksonline.com/2012ALENEX/data/papers/020.pdf.

Toggle abstract

@InProceedings{HMSSS2012,
AUTHOR = {Huber, Katharina and Moulton, Vincent and Spillner, Andreas and Storandt, Sabine and Suchecki, Radoslaw},
TITLE = {Computing a consensus of multilabeled trees},
YEAR = {2012},
BOOKTITLE = {ALENEX12},
PAGES = {84-92},
URL = {http://dx.doi.org/10.1137/1.9781611972924.9},
NOTE = {http://siam.omnibooksonline.com/2012ALENEX/data/papers/020.pdf},
KEYWORDS = {duplication, explicit network, exponential algorithm, phylogenetic network, phylogeny}
}

50

Cayla McBee. Generalizing Fourier Calculus on Evolutionary Trees to Splits Networks. In ISPAN'12, Pages 149-155, 2012.
Keywords: abstract network, from sequences, phylogenetic network, phylogeny, split network, statistical model.

Toggle abstract

@InProceedings{McBee2012,
AUTHOR = {McBee, Cayla},
TITLE = {Generalizing Fourier Calculus on Evolutionary Trees to Splits Networks},
YEAR = {2012},
BOOKTITLE = {ISPAN'12},
PAGES = {149-155},
URL = {http://dx.doi.org/10.1109/I-SPAN.2012.28},
KEYWORDS = {abstract network, from sequences, phylogenetic network, phylogeny, split network, statistical model}
}

51

Alix Boc. Détection des transferts horizontaux de gènes : modèles et algorithmes appliqués à l'évolution des espèces et des langues. PhD thesis, Université du Québec à Montréal, Canada, 2012.
Keywords: explicit network, from rooted trees, from species tree, phylogenetic network, phylogeny, Program T REX, reconstruction.
Note: http://www.collectionscanada.gc.ca/obj/thesescanada/vol2/QMUQ/TC-QMUQ-4658.pdf.

@PhdThesis{Boc2012,
AUTHOR = {Boc, Alix},
TITLE = {D{\~A}�tection des transferts horizontaux de g{\~A}�nes : mod{\~A}�les et algorithmes appliqu{\~A}�s {\~A}� l'{\~A}�volution des esp{\~A}�ces et des langues},
YEAR = {2012},
SCHOOL = {Universit{\~A}� du Qu{\~A}�bec {\~A}� Montr{\~A}�al, Canada},
URL = {http://www.collectionscanada.gc.ca/obj/thesescanada/vol2/QMUQ/TC-QMUQ-4658.pdf},
NOTE = {http://www.collectionscanada.gc.ca/obj/thesescanada/vol2/QMUQ/TC-QMUQ-4658.pdf},
KEYWORDS = {explicit network, from rooted trees, from species tree, phylogenetic network, phylogeny, Program T REX, reconstruction}
}

52

Fenglou Mao, David Williams, Olga Zhaxybayeva, Maria S. Poptsova, Pascal Lapierre, J. Peter Gogarten and Ying Xu. Quartet decomposition server: a platform for analyzing phylogenetic trees. In BMCB, Vol. 13:123, 2012.
Keywords: abstract network, from quartets, phylogenetic network, phylogeny, Program Quartet Decomposition, reconstruction, software, split network.

Toggle abstract

@Article{MWZPLGX2012,
AUTHOR = {Mao, Fenglou and Williams, David and Zhaxybayeva, Olga and Poptsova, Maria S. and Lapierre, Pascal and Gogarten, J. Peter and Xu, Ying},
TITLE = {Quartet decomposition server: a platform for analyzing phylogenetic trees},
YEAR = {2012},
JOURNAL = {BMCB},
VOLUME = {13},
PAGES = {123},
URL = {http://dx.doi.org/10.1186/1471-2105-13-123},
KEYWORDS = {abstract network, from quartets, phylogenetic network, phylogeny, Program Quartet Decomposition, reconstruction, software, split network}
}

53

Donovan H. Parks and Robert G. Beiko. Measuring Community Similarity with Phylogenetic Networks. In MBE, Vol. 29(12):3947-3958, 2012.
Keywords: abstract network, diversity, phylogenetic network, phylogeny, split network.
Note: poster available at http://dparks.wdfiles.com/local--files/publications/SMBE_BetaDiversity_2011.pdf.

Toggle abstract

@Article{ParksBeiko2012,
AUTHOR = {Parks, Donovan H. and Beiko, Robert G.},
TITLE = {Measuring Community Similarity with Phylogenetic Networks},
YEAR = {2012},
JOURNAL = {MBE},
VOLUME = {29},
NUMBER = {12},
PAGES = {3947-3958},
URL = {http://dx.doi.org/10.1093/molbev/mss200},
NOTE = {poster available at http://dparks.wdfiles.com/local--files/publications/SMBE_BetaDiversity_2011.pdf},
KEYWORDS = {abstract network, diversity, phylogenetic network, phylogeny, split network}
}

54

Zhi-Zhong Chen, Fei Deng and Lusheng Wang. Simultaneous Identification of Duplications, Losses, and Lateral Gene Transfers. In TCBB, Vol. 9(5):1515-1528, 2012.
Keywords: duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction.
Note: http://www.cs.cityu.edu.hk/~lwang/research/tcbb2012c.pdf.

Toggle abstract

@Article{CDW2012,
AUTHOR = {Chen, Zhi-Zhong and Deng, Fei and Wang, Lusheng},
TITLE = {Simultaneous Identification of Duplications, Losses, and Lateral Gene Transfers},
YEAR = {2012},
JOURNAL = {TCBB},
VOLUME = {9},
NUMBER = {5},
PAGES = {1515-1528},
URL = {http://dx.doi.org/10.1109/TCBB.2012.79},
NOTE = {http://www.cs.cityu.edu.hk/~lwang/research/tcbb2012c.pdf},
KEYWORDS = {duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction}
}

55

Matthieu Willems. Un nouvel algorithme pour l'inférence de réseaux d'hybridation. Master's thesis, Université du Québec à Montréal, Canada, 2012.
Keywords: explicit network, from distances, heuristic, phylogenetic network, phylogeny, reconstruction.
Note: http://www.archipel.uqam.ca/5015/.

@MastersThesis{Willems2012,
AUTHOR = {Willems, Matthieu},
TITLE = {Un nouvel algorithme pour l'inf{\~A}�rence de r{\~A}�seaux d'hybridation},
YEAR = {2012},
SCHOOL = {Universit{\~A}� du Qu{\~A}�bec {\~A}� Montr{\~A}�al, Canada},
URL = {http://www.archipel.uqam.ca/5015/},
NOTE = {http://www.archipel.uqam.ca/5015/},
KEYWORDS = {explicit network, from distances, heuristic, phylogenetic network, phylogeny, reconstruction}
}

2011

1

Daniel H. Huson and Celine Scornavacca. A survey of combinatorial methods for phylogenetic networks. In Genome Biology and Evolution, Vol. 3:23-35, 2011.
Keywords: phylogenetic network, survey.
Note: http://dx.doi.org/10.1093/gbe/evq077.

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@Article{HusonScornavacca2011,
AUTHOR = {Huson, Daniel H. and Scornavacca, Celine},
TITLE = {A survey of combinatorial methods for phylogenetic networks},
YEAR = {2011},
JOURNAL = {Genome Biology and Evolution},
VOLUME = {3},
PAGES = {23-35},
URL = {http://dx.doi.org/10.1093/gbe/evq077},
NOTE = {http://dx.doi.org/10.1093/gbe/evq077},
KEYWORDS = {phylogenetic network, survey}
}

2

Ali Tofigh, Mike Hallett and Jens Lagergren. Simultaneous Identification of Duplications and Lateral Gene Transfers. In TCBB, Vol. 8(2):517-535, 2011.
Keywords: duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1109/TCBB.2010.14.

Toggle abstract

@Article{THL2011,
AUTHOR = {Tofigh, Ali and Hallett, Mike and Lagergren, Jens},
TITLE = {Simultaneous Identification of Duplications and Lateral Gene Transfers},
YEAR = {2011},
JOURNAL = {TCBB},
VOLUME = {8},
NUMBER = {2},
PAGES = {517-535},
URL = {http://dx.doi.org/10.1109/TCBB.2010.14},
NOTE = {http://dx.doi.org/10.1109/TCBB.2010.14},
KEYWORDS = {duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction}
}

3

Dan Levy and Lior Pachter. The Neighbor-Net Algorithm. In Advances in Applied Mathematics, Vol. 47(2):240-258, 2011.
Keywords: abstract network, circular split system, evaluation, from distances, NeighborNet, phylogenetic network, phylogeny, split network.
Note: http://arxiv.org/abs/math/0702515.

Toggle abstract

@Article{LevyPachter2008,
AUTHOR = {Levy, Dan and Pachter, Lior},
TITLE = {The Neighbor-Net Algorithm},
YEAR = {2011},
JOURNAL = {Advances in Applied Mathematics},
VOLUME = {47},
NUMBER = {2},
PAGES = {240-258},
URL = {http://dx.doi.org/10.1016/j.aam.2010.09.002},
NOTE = {http://arxiv.org/abs/math/0702515},
ANNOTE = {BIBUPDATE : 20080321},
KEYWORDS = {abstract network, circular split system, evaluation, from distances, NeighborNet, phylogenetic network, phylogeny, split network}
}

4

Shlomo Moran, Sagi Snir and Wing-Kin Sung. Partial Convex Recolorings of Trees and Galled Networks: Tight Upper and Lower bounds. In ACM Transactions on Algorithms, Vol. 7(4), 2011.
Keywords: evaluation, galled tree, phylogenetic network.
Note: http://www.cs.technion.ac.il/~moran/r/PS/gnets-TOA-7Feb2007.pdf.

Toggle abstract

@Article{MSS2011,
AUTHOR = {Moran, Shlomo and Snir, Sagi and Sung, Wing-Kin},
TITLE = {Partial Convex Recolorings of Trees and Galled Networks: Tight Upper and Lower bounds},
YEAR = {2011},
JOURNAL = {ACM Transactions on Algorithms},
VOLUME = {7},
NUMBER = {4},
URL = {http://dx.doi.org/10.1145/2000807.2000810},
NOTE = {http://www.cs.technion.ac.il/~moran/r/PS/gnets-TOA-7Feb2007.pdf},
ANNOTE = {BIBUPDATE : 20080605, http://www.cs.technion.ac.il/~moran/r/PS/TALG-20Nov2008.pdf},
KEYWORDS = {evaluation, galled tree, phylogenetic network}
}

5

Gabriel Cardona, Mercè Llabrés, Francesc Rosselló and Gabriel Valiente. Comparison of Galled Trees. In TCBB, Vol. 8(2):410-427, 2011.
Note: http://arxiv.org/abs/0906.1166.

Toggle abstract

@Article{CLRV2011,
AUTHOR = {Cardona, Gabriel and Llabr{\~A}�s, Merc{\~A}� and Rossell{\~A}�, Francesc and Valiente, Gabriel},
TITLE = {Comparison of Galled Trees},
YEAR = {2011},
JOURNAL = {TCBB},
VOLUME = {8},
NUMBER = {2},
PAGES = {410-427},
URL = {http://dx.doi.org/10.1109/TCBB.2010.60},
NOTE = {http://arxiv.org/abs/0906.1166}
}

6

Daniel H. Huson, Regula Rupp and Celine Scornavacca. Phylogenetic Networks: Concepts, Algorithms and Applications. Cambridge University Press, 2011.
Keywords: phylogenetic network, phylogeny, survey.
Note: http://www.phylogenetic-networks.org/, buy at Amazon.com. Reviews here and there.

@Book{HRS2011,
AUTHOR = {Huson, Daniel H. and Rupp, Regula and Scornavacca, Celine},
TITLE = {Phylogenetic Networks: Concepts, Algorithms and Applications},
YEAR = {2011},
PUBLISHER = {Cambridge University Press},
NOTE = {http://www.phylogenetic-networks.org/, buy at Amazon.com. Reviews here and there},
KEYWORDS = {phylogenetic network, phylogeny, survey}
}

7

Katharina Huber, Leo van Iersel, Steven Kelk and Radoslaw Suchecki. A Practical Algorithm for Reconstructing Level-1 Phylogenetic Networks. In TCBB, Vol. 8(3):607-620, 2011.
Keywords: explicit network, from triplets, galled tree, generation, heuristic, phylogenetic network, phylogeny, Program LEV1ATHAN, Program Lev1Generator, reconstruction, software.
Note: http://arxiv.org/abs/0910.4067.

Toggle abstract

@Article{HIKS2011,
AUTHOR = {Huber, Katharina and van Iersel, Leo and Kelk, Steven and Suchecki, Radoslaw},
TITLE = {A Practical Algorithm for Reconstructing Level-1 Phylogenetic Networks},
YEAR = {2011},
JOURNAL = {TCBB},
VOLUME = {8},
NUMBER = {3},
PAGES = {607-620},
URL = {http://dx.doi.org/10.1109/TCBB.2010.17},
NOTE = {http://arxiv.org/abs/0910.4067},
KEYWORDS = {explicit network, from triplets, galled tree, generation, heuristic, phylogenetic network, phylogeny, Program LEV1ATHAN, Program Lev1Generator, reconstruction, software}
}

8

Josh Voorkamp né Collins, Simone Linz and Charles Semple. Quantifying hybridization in realistic time. In JCB, Vol. 18(10):1305-1318, 2011.
Keywords: explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, software.
Note: http://wwwcsif.cs.ucdavis.edu/~linzs/CLS10_interleave.pdf, software available at http://www.math.canterbury.ac.nz/~c.semple/software.shtml.

Toggle abstract

@Article{CLS2011,
AUTHOR = {Voorkamp n{\~A}� Collins, Josh and Linz, Simone and Semple, Charles},
TITLE = {Quantifying hybridization in realistic time},
YEAR = {2011},
JOURNAL = {JCB},
VOLUME = {18},
NUMBER = {10},
PAGES = {1305-1318},
URL = {http://dx.doi.org/10.1089/cmb.2009.0166},
NOTE = {http://wwwcsif.cs.ucdavis.edu/~linzs/CLS10_interleave.pdf, software available at http://www.math.canterbury.ac.nz/~c.semple/software.shtml},
KEYWORDS = {explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, software}
}

9

Leo van Iersel and Steven Kelk. Constructing the Simplest Possible Phylogenetic Network from Triplets. In ALG, Vol. 60(2):207-235, 2011.
Keywords: explicit network, from triplets, galled tree, level k phylogenetic network, minimum number, phylogenetic network, phylogeny, polynomial, Program Marlon, Program Simplistic.
Note: http://dx.doi.org/10.1007/s00453-009-9333-0.

Toggle abstract

@Article{IerselKelk2011b,
AUTHOR = {van Iersel, Leo and Kelk, Steven},
TITLE = {Constructing the Simplest Possible Phylogenetic Network from Triplets},
YEAR = {2011},
JOURNAL = {ALG},
VOLUME = {60},
NUMBER = {2},
PAGES = {207-235},
URL = {http://dx.doi.org/10.1007/s00453-009-9333-0},
NOTE = {http://dx.doi.org/10.1007/s00453-009-9333-0},
KEYWORDS = {explicit network, from triplets, galled tree, level k phylogenetic network, minimum number, phylogenetic network, phylogeny, polynomial, Program Marlon, Program Simplistic}
}

10

Jean-Philippe Doyon, Celine Scornavacca, Konstantin Yu Gorbunov, Gergely J. Szöllösi, Vincent Ranwez and Vincent Berry. An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications, and transfers. In Proceedings of the Eighth RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG'10), Vol. 6398:93-108 of LNCS, springer, 2011.
Keywords: branch length, duplication, dynamic programming, explicit network, from multilabeled tree, from species tree, from unrooted trees, lateral gene transfer, loss, phylogenetic network, phylogeny, polynomial, Program Mowgli, reconstruction.
Note: http://www.lirmm.fr/~vberry/Publis/MPR-DoyonEtAl.pdf, software available at http://www.atgc-montpellier.fr/MPR/.

Toggle abstract

@InProceedings{DSGSRB2010,
AUTHOR = {Doyon, Jean-Philippe and Scornavacca, Celine and Gorbunov, Konstantin Yu and Sz{\~A}�ll{\~A}�si, Gergely J. and Ranwez, Vincent and Berry, Vincent},
TITLE = {An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications, and transfers},
YEAR = {2011},
BOOKTITLE = {Proceedings of the Eighth RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG'10)},
VOLUME = {6398},
PAGES = {93-108},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-642-16181-0_9},
NOTE = {http://www.lirmm.fr/~vberry/Publis/MPR-DoyonEtAl.pdf, software available at http://www.atgc-montpellier.fr/MPR/},
KEYWORDS = {branch length, duplication, dynamic programming, explicit network, from multilabeled tree, from species tree, from unrooted trees, lateral gene transfer, loss, phylogenetic network, phylogeny, polynomial, Program Mowgli, reconstruction}
}

11

Leo van Iersel and Steven Kelk. When two trees go to war. In JTB, Vol. 269(1):245-255, 2011.
Keywords: APX hard, explicit network, from clusters, from rooted trees, from sequences, from triplets, level k phylogenetic network, minimum number, NP complete, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://arxiv.org/abs/1004.5332.

Toggle abstract

@Article{IerselKelk2011,
AUTHOR = {van Iersel, Leo and Kelk, Steven},
TITLE = {When two trees go to war},
YEAR = {2011},
JOURNAL = {JTB},
VOLUME = {269},
NUMBER = {1},
PAGES = {245-255},
URL = {http://dx.doi.org/10.1016/j.jtbi.2010.10.032},
NOTE = {http://arxiv.org/abs/1004.5332},
KEYWORDS = {APX hard, explicit network, from clusters, from rooted trees, from sequences, from triplets, level k phylogenetic network, minimum number, NP complete, phylogenetic network, phylogeny, polynomial, reconstruction}
}

12

Stephen J. Willson. Restricted trees: simplifying networks with bottlenecks. In BMB, Vol. 73(10):2322-2338, 2011.
Keywords: from network, phylogenetic network.
Note: http://arxiv.org/abs/1005.4956.

Toggle abstract

@Article{Willson2011,
AUTHOR = {Willson, Stephen J.},
TITLE = {Restricted trees: simplifying networks with bottlenecks},
YEAR = {2011},
JOURNAL = {BMB},
VOLUME = {73},
NUMBER = {10},
PAGES = {2322-2338},
URL = {http://dx.doi.org/10.1007/s11538-010-9624-2},
NOTE = {http://arxiv.org/abs/1005.4956},
KEYWORDS = {from network, phylogenetic network}
}

13

Mukul S. Bansal, J. Peter Gogarten and Ron Shamir. Detecting Highways of Horizontal Gene Transfer. In Proceedings of the Eighth RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG'10), Vol. 6398:109-120 of LNCS, springer, 2011.
Keywords: explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.cs.iastate.edu/~bansal/Highways_RCG10.pdf.

Toggle abstract

@InProceedings{BGS2010,
AUTHOR = {Bansal, Mukul S. and Gogarten, J. Peter and Shamir, Ron},
TITLE = {Detecting Highways of Horizontal Gene Transfer},
YEAR = {2011},
BOOKTITLE = {Proceedings of the Eighth RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG'10)},
VOLUME = {6398},
PAGES = {109-120},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-642-16181-0_10},
NOTE = {http://www.cs.iastate.edu/~bansal/Highways_RCG10.pdf},
KEYWORDS = {explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, polynomial, reconstruction}
}

14

Ruzbeh Tusserkani, Changiz Eslahchi, Hadi Poormohammadi and Azin Azadi. TripNet: A Method for Constructing Phylogenetic Networks from Triplets. 2011.
Keywords: explicit network, heuristic, level k phylogenetic network, phylogenetic network, phylogeny, Program TripNet, reconstruction, software.
Note: http://arxiv.org/abs/1104.4720.

@Misc{TEPA2011,
AUTHOR = {Tusserkani, Ruzbeh and Eslahchi, Changiz and Poormohammadi, Hadi and Azadi, Azin},
TITLE = {TripNet: A Method for Constructing Phylogenetic Networks from Triplets},
YEAR = {2011},
NOTE = {http://arxiv.org/abs/1104.4720},
KEYWORDS = {explicit network, heuristic, level k phylogenetic network, phylogenetic network, phylogeny, Program TripNet, reconstruction, software}
}

15

Marc Thuillard and Vincent Moulton. Identifying and reconstructing lateral transfers from distance matrices by combining the Minimum Contradiction Method and Neighbor-Net. In JBCB, Vol. 9(4):453-470, 2011.
Keywords: from distances, lateral gene transfer, minimum contradiction, NeighborNet, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1142/S0219720011005409, slides available at http://www.newton.ac.uk/programmes/PLG/seminars/062015501.html.

Toggle abstract

@Article{ThuillardMoulton2011,
AUTHOR = {Thuillard, Marc and Moulton, Vincent},
TITLE = {Identifying and reconstructing lateral transfers from distance matrices by combining the Minimum Contradiction Method and Neighbor-Net},
YEAR = {2011},
JOURNAL = {JBCB},
VOLUME = {9},
NUMBER = {4},
PAGES = {453-470},
URL = {http://dx.doi.org/10.1142/S0219720011005409},
NOTE = {http://dx.doi.org/10.1142/S0219720011005409, slides available at http://www.newton.ac.uk/programmes/PLG/seminars/062015501.html},
KEYWORDS = {from distances, lateral gene transfer, minimum contradiction, NeighborNet, phylogenetic network, phylogeny, reconstruction}
}

16

Klaus Schliep. Phangorn: Phylogenetic analysis in R. In Bioinformatics, Vol. 27(4):592-593, 2011.
Keywords: abstract network, from distances, phylogenetic network, Program Phangorn, software, split, split network.
Note: http://dx.doi.org/10.1093/bioinformatics/btq706.

Toggle abstract

@Article{Schliep2011,
AUTHOR = {Schliep, Klaus},
TITLE = {Phangorn: Phylogenetic analysis in R},
YEAR = {2011},
JOURNAL = {Bioinformatics},
VOLUME = {27},
NUMBER = {4},
PAGES = {592-593},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq706},
NOTE = {http://dx.doi.org/10.1093/bioinformatics/btq706},
KEYWORDS = {abstract network, from distances, phylogenetic network, Program Phangorn, software, split, split network}
}

17

Lavanya Kannan, Hua Li and Arcady Mushegian. A Polynomial-Time Algorithm Computing Lower and Upper Bounds of the Rooted Subtree Prune and Regraft Distance. In JCB, Vol. 18(5):743-757, 2011.
Keywords: bound, minimum number, polynomial, SPR distance.
Note: http://dx.doi.org/10.1089/cmb.2010.0045.

Toggle abstract

@Article{KLM2011,
AUTHOR = {Kannan, Lavanya and Li, Hua and Mushegian, Arcady},
TITLE = {A Polynomial-Time Algorithm Computing Lower and Upper Bounds of the Rooted Subtree Prune and Regraft Distance},
YEAR = {2011},
JOURNAL = {JCB},
VOLUME = {18},
NUMBER = {5},
PAGES = {743-757},
URL = {http://dx.doi.org/10.1089/cmb.2010.0045},
NOTE = {http://dx.doi.org/10.1089/cmb.2010.0045},
KEYWORDS = {bound, minimum number, polynomial, SPR distance}
}

18

Yun Yu, Cuong Than, James H. Degnan and Luay Nakhleh. Coalescent Histories on Phylogenetic Networks and Detection of Hybridization Despite Incomplete Lineage Sorting. In Systematic Biology, Vol. 60(2):138-149, 2011.
Keywords: coalescent, hybridization, lineage sorting, reconstruction, statistical model.
Note: http://www.cs.rice.edu/~nakhleh/Papers/YuEtAl-SB11.pdf.

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@Article{YTDN2011,
AUTHOR = {Yu, Yun and Than, Cuong and Degnan, James H. and Nakhleh, Luay},
TITLE = {Coalescent Histories on Phylogenetic Networks and Detection of Hybridization Despite Incomplete Lineage Sorting},
YEAR = {2011},
JOURNAL = {Systematic Biology},
VOLUME = {60},
NUMBER = {2},
PAGES = {138-149},
URL = {http://dx.doi.org/10.1093/sysbio/syq084},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/YuEtAl-SB11.pdf},
KEYWORDS = {coalescent, hybridization, lineage sorting, reconstruction, statistical model}
}

19

Celine Scornavacca, Franziska Zickmann and Daniel H. Huson. Tanglegrams for Rooted Phylogenetic Trees and Networks. In ISMB11, Vol. 27(13):i248-i256 of BIO, 2011.
Keywords: from network, heuristic, integer linear programming, phylogenetic network, phylogeny, Program Dendroscope, tanglegram, visualization.
Note: http://dx.doi.org/10.1093/bioinformatics/btr210.

Toggle abstract

@InProceedings{ScornavaccaHuson2011,
AUTHOR = {Scornavacca, Celine and Zickmann, Franziska and Huson, Daniel H.},
TITLE = {Tanglegrams for Rooted Phylogenetic Trees and Networks},
YEAR = {2011},
BOOKTITLE = {ISMB11},
VOLUME = {27},
NUMBER = {13},
PAGES = {i248-i256},
SERIES = {BIO},
URL = {http://dx.doi.org/10.1093/bioinformatics/btr210},
NOTE = {http://dx.doi.org/10.1093/bioinformatics/btr210},
KEYWORDS = {from network, heuristic, integer linear programming, phylogenetic network, phylogeny, Program Dendroscope, tanglegram, visualization}
}

20

Sha Zhu, James H. Degnan and Mike Steel. Probabilistic modeling of gene trees given species networks. 2011.
Keywords: from network, generation, phylogenetic network, phylogeny, statistical model.
Note: Poster, http://www.newton.ac.uk/programmes/PLG/Zhu.pdf.

@Misc{ZDS2011,
AUTHOR = {Zhu, Sha and Degnan, James H. and Steel, Mike},
TITLE = {Probabilistic modeling of gene trees given species networks},
YEAR = {2011},
NOTE = {Poster, http://www.newton.ac.uk/programmes/PLG/Zhu.pdf},
KEYWORDS = {from network, generation, phylogenetic network, phylogeny, statistical model}
}

21

Gergely J. Szöllösi and Vincent Daubin. Modeling Gene Family Evolution and Reconciling Phylogenetic Discord. In Evolutionary Genomics, Statistical and Computational Methods, Volume 2, Methods in Molecular Biology, Vol. 856:29-51, Chapter 2, springer, 2011.
Keywords: duplication, from multilabeled tree, lateral gene transfer, likelihood, phylogeny, reconstruction, statistical model.
Note: ArXiv version entitled The pattern and process of gene family evolution.

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@Article{GergelyDaubin2011,
AUTHOR = {Sz{\~A}�ll{\~A}�si, Gergely J. and Daubin, Vincent},
TITLE = {Modeling Gene Family Evolution and Reconciling Phylogenetic Discord},
YEAR = {2011},
JOURNAL = {Methods in Molecular Biology},
BOOKTITLE = {Evolutionary Genomics, Statistical and Computational Methods, Volume 2},
VOLUME = {856},
PAGES = {29-51},
PUBLISHER = {springer},
CHAPTER = {2},
URL = {http://dx.doi.org/10.1007/978-1-61779-585-5_2},
NOTE = {ArXiv version entitled The pattern and process of gene family evolution},
KEYWORDS = {duplication, from multilabeled tree, lateral gene transfer, likelihood, phylogeny, reconstruction, statistical model}
}

22

Lawrence A. David and Eric J. Alm. Rapid evolutionary innovation during an Archaean genetic expansion. In Nature, Vol. 469:93-96, 2011.
Keywords: duplication, dynamic programming, from multilabeled tree, from rooted trees, from species tree, parsimony, phylogenetic network, phylogeny, Program Angst.
Note: http://dx.doi.org/10.1038/nature09649, Program Angst described here.

@Article{DavidAlm2011,
AUTHOR = {David, Lawrence A. and Alm, Eric J.},
TITLE = {Rapid evolutionary innovation during an Archaean genetic expansion},
YEAR = {2011},
JOURNAL = {Nature},
VOLUME = {469},
PAGES = {93-96},
URL = {http://dx.doi.org/10.1038/nature09649},
NOTE = {http://dx.doi.org/10.1038/nature09649, Program Angst described here},
KEYWORDS = {duplication, dynamic programming, from multilabeled tree, from rooted trees, from species tree, parsimony, phylogenetic network, phylogeny, Program Angst}
}

23

Steven Kelk. A note on efficient computation of hybridization number via softwired clusters. 2011.
Keywords: explicit network, FPT, from clusters, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1108.4642.

@Misc{Kelk2011,
AUTHOR = {Kelk, Steven},
TITLE = {A note on efficient computation of hybridization number via softwired clusters},
YEAR = {2011},
NOTE = {http://arxiv.org/abs/1108.4642},
KEYWORDS = {explicit network, FPT, from clusters, phylogenetic network, phylogeny, reconstruction}
}

24

Paul Phipps. Planar phylogenetic network optimization. PhD thesis, University of Texas at Dallas, U.S.A., 2011.
Keywords: abstract network, from distances, phylogenetic network, Program PhippsNetwork, split, split network.
Note: http://proquest.umi.com/pqdlink?did=2337197411&Fmt=7&clientId=176295&RQT=309&VName=PQD.

@PhdThesis{Phipps2011,
AUTHOR = {Phipps, Paul},
TITLE = {Planar phylogenetic network optimization},
YEAR = {2011},
SCHOOL = {University of Texas at Dallas, U.S.A.},
NOTE = {http://proquest.umi.com/pqdlink?did=2337197411{\&}Fmt=7{\&}clientId=176295{\&}RQT=309{\&}VName=PQD},
KEYWORDS = {abstract network, from distances, phylogenetic network, Program PhippsNetwork, split, split network}
}

25

Puspal Bhabak. Improving the approximation ratio of the maximum agreement forest (MAF) on k trees and estimating the approximation ratio of the acyclic-MAF on k trees. Master's thesis, University of Windsor, Canada, 2011.
Keywords: agreement forest, approximation, explicit network, from rooted trees, phylogenetic network, phylogeny, reconstruction.
Note: http://scholar.uwindsor.ca/cgi/viewcontent.cgi?article=1315&context=etd.

@MastersThesis{Bhabak2011,
AUTHOR = {Bhabak, Puspal},
TITLE = {Improving the approximation ratio of the maximum agreement forest (MAF) on k trees and estimating the approximation ratio of the acyclic-MAF on k trees},
YEAR = {2011},
SCHOOL = {University of Windsor, Canada},
URL = {http://scholar.uwindsor.ca/cgi/viewcontent.cgi?article=1315{\&}amp;context=etd},
NOTE = {http://scholar.uwindsor.ca/cgi/viewcontent.cgi?article=1315{\&}context=etd},
KEYWORDS = {agreement forest, approximation, explicit network, from rooted trees, phylogenetic network, phylogeny, reconstruction}
}

26

Mukul S. Bansal, Guy Banay, J. Peter Gogarten and Ron Shamir. Detecting Highways of Horizontal Gene Transfer. In JCB, Vol. 18(9):1087-1114, 2011.
Keywords: explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://people.csail.mit.edu/mukul/HighwayFull_preprint.pdf.

Toggle abstract

@Article{BBGS2011,
AUTHOR = {Bansal, Mukul S. and Banay, Guy and Gogarten, J. Peter and Shamir, Ron},
TITLE = {Detecting Highways of Horizontal Gene Transfer},
YEAR = {2011},
JOURNAL = {JCB},
VOLUME = {18},
NUMBER = {9},
PAGES = {1087-1114},
URL = {http://dx.doi.org/10.1089/cmb.2011.0066},
NOTE = {http://people.csail.mit.edu/mukul/HighwayFull_preprint.pdf},
KEYWORDS = {explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, polynomial, reconstruction}
}

27

Thu-Hien To. On some graph problems in phylogenetics. PhD thesis, Université Paris Diderot - Paris 7, France, 2011.
Keywords: explicit network, from triplets, level k phylogenetic network, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.liafa.jussieu.fr/~toth/thesis.pdf.

@PhdThesis{To2011,
AUTHOR = {To, Thu-Hien},
TITLE = {On some graph problems in phylogenetics},
YEAR = {2011},
SCHOOL = {Universit{\~A}� Paris Diderot - Paris 7, France},
NOTE = {http://www.liafa.jussieu.fr/~toth/thesis.pdf},
KEYWORDS = {explicit network, from triplets, level k phylogenetic network, phylogenetic network, phylogeny, polynomial, reconstruction}
}

28

Alethea Rea. Statistical approaches to phylogenetic networks, recombination and testing of incongruence. PhD thesis, The University of Auckland, New Zealand, 2011.
Keywords: abstract network, AIC, BIC, phylogenetic network, phylogeny, split, split network, statistical model.
Note: https://researchspace.auckland.ac.nz/handle/2292/67624.

@PhdThesis{Rea2011,
AUTHOR = {Rea, Alethea},
TITLE = {Statistical approaches to phylogenetic networks, recombination and testing of incongruence},
YEAR = {2011},
SCHOOL = {The University of Auckland, New Zealand},
NOTE = {https://researchspace.auckland.ac.nz/handle/2292/67624},
KEYWORDS = {abstract network, AIC, BIC, phylogenetic network, phylogeny, split, split network, statistical model}
}

29

Rosalba Radice. A Bayesian Approach to Phylogenetic Networks. PhD thesis, University of Bath, U.K., 2011.
Keywords: bayesian, explicit network, from sequences, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: http://opus.bath.ac.uk/25521/.

@PhdThesis{Radice2011,
AUTHOR = {Radice, Rosalba},
TITLE = {A Bayesian Approach to Phylogenetic Networks},
YEAR = {2011},
SCHOOL = {University of Bath, U.K.},
NOTE = {http://opus.bath.ac.uk/25521/},
KEYWORDS = {bayesian, explicit network, from sequences, phylogenetic network, phylogeny, reconstruction, statistical model}
}

30

Jean-Philippe Doyon, Vincent Ranwez, Vincent Daubin and Vincent Berry. Models, algorithms and programs for phylogeny reconciliation. In Briefings in Bioinformatics, Vol. 12(5):392-400, 2011.
Keywords: explicit network, lateral gene transfer, phylogenetic network, phylogeny, reconstruction, survey.

Toggle abstract

@Article{DRDB2011,
AUTHOR = {Doyon, Jean-Philippe and Ranwez, Vincent and Daubin, Vincent and Berry, Vincent},
TITLE = {Models, algorithms and programs for phylogeny reconciliation},
YEAR = {2011},
JOURNAL = {Briefings in Bioinformatics},
VOLUME = {12},
NUMBER = {5},
PAGES = {392-400},
URL = {http://dx.doi.org/10.1093/bib/bbr045},
KEYWORDS = {explicit network, lateral gene transfer, phylogenetic network, phylogeny, reconstruction, survey}
}

31

Alix Boc and Vladimir Makarenkov. Towards an accurate identification of mosaic genes and partial horizontal gene transfers. In NAR, Vol. 39(21):e144, 2011.
Keywords: explicit network, from sequences, lateral gene transfer, phylogenetic network, phylogeny, Program T REX, reconstruction.
Note: http://dx.doi.org/10.1093/nar/gkr735.

Toggle abstract

@Article{BocMakarenkov2011,
AUTHOR = {Boc, Alix and Makarenkov, Vladimir},
TITLE = {Towards an accurate identification of mosaic genes and partial horizontal gene transfers},
YEAR = {2011},
JOURNAL = {NAR},
VOLUME = {39},
NUMBER = {21},
PAGES = {e144},
URL = {http://dx.doi.org/10.1093/nar/gkr735},
NOTE = {http://dx.doi.org/10.1093/nar/gkr735},
KEYWORDS = {explicit network, from sequences, lateral gene transfer, phylogenetic network, phylogeny, Program T REX, reconstruction}
}

32

David A. Morrison. Introduction to Phylogenetic Networks. RJR Productions, 2011.
Keywords: phylogenetic network, phylogeny, reconstruction, survey.
Note: http://www.rjr-productions.org/Networks/Download.html.

@Book{Morrison2011,
AUTHOR = {Morrison, David A.},
TITLE = {Introduction to Phylogenetic Networks},
YEAR = {2011},
PUBLISHER = {RJR Productions},
NOTE = {http://www.rjr-productions.org/Networks/Download.html},
KEYWORDS = {phylogenetic network, phylogeny, reconstruction, survey}
}

33

Changiz Eslahchi and Reza Hassanzadeh. New Algorithm for Constructing Supernetworks from Partial Trees. In MCCMB11, Pages 106-107, 2011.
Keywords: abstract network, from unrooted trees, heuristic, phylogenetic network, phylogeny, Program SNSA, reconstruction, simulated annealing, split network.
Note: http://mccmb.belozersky.msu.ru/2011/mccmb11.pdf#page=106.

@InProceedings{EslahchiHassanzadeh2011,
AUTHOR = {Eslahchi, Changiz and Hassanzadeh, Reza},
TITLE = {New Algorithm for Constructing Supernetworks from Partial Trees},
YEAR = {2011},
BOOKTITLE = {MCCMB11},
PAGES = {106-107},
NOTE = {http://mccmb.belozersky.msu.ru/2011/mccmb11.pdf#page=106},
KEYWORDS = {abstract network, from unrooted trees, heuristic, phylogenetic network, phylogeny, Program SNSA, reconstruction, simulated annealing, split network}
}

34

Miro Ferreri, Weijie Qu and Bo Han. Phylogenetic networks: A tool to display character conflict and demographic history. In African Journal of Biotechnology , Vol. 10(60):12799-12803, 2011.
Keywords: phylogenetic network, phylogeny, survey, visualization.

@Article{FQH2011,
AUTHOR = {Ferreri, Miro and Qu, Weijie and Han, Bo},
TITLE = {Phylogenetic networks: A tool to display character conflict and demographic history},
YEAR = {2011},
JOURNAL = {African Journal of Biotechnology },
VOLUME = {10},
NUMBER = {60},
PAGES = {12799-12803},
URL = {http://dx.doi.org/10.5897/AJB11.010},
KEYWORDS = {phylogenetic network, phylogeny, survey, visualization}
}

35

Benjamin Albrecht. Fast Computation of Hybridization Networks. Master's thesis, University of Tübingen, Germany, 2011.
Keywords: explicit network, from rooted trees, minimum number, phylogenetic network, phylogeny, reconstruction.

@MastersThesis{Albrecht2011,
AUTHOR = {Albrecht, Benjamin},
TITLE = {Fast Computation of Hybridization Networks},
YEAR = {2011},
SCHOOL = {University of T{\~A}�bingen, Germany},
KEYWORDS = {explicit network, from rooted trees, minimum number, phylogenetic network, phylogeny, reconstruction}
}

36

Louxin Zhang, Yen Kaow Ng, Taoyang Wu and Yu Zheng. Network model and efficient method for detecting relative duplications or horizontal gene transfers. In ICCABS11, Pages 214-219, 2011.
Keywords: dynamic programming, explicit network, from network, from rooted trees, from species tree, phylogenetic network, phylogeny, polynomial, reconstruction.

Toggle abstract

@InProceedings{ZNWZ2011,
AUTHOR = {Zhang, Louxin and Ng, Yen Kaow and Wu, Taoyang and Zheng, Yu},
TITLE = {Network model and efficient method for detecting relative duplications or horizontal gene transfers},
YEAR = {2011},
BOOKTITLE = {ICCABS11},
PAGES = {214-219},
URL = {http://dx.doi.org/10.1109/ICCABS.2011.5729883 },
KEYWORDS = {dynamic programming, explicit network, from network, from rooted trees, from species tree, phylogenetic network, phylogeny, polynomial, reconstruction}
}

2010

1

Jaroslaw Byrka, Pawel Gawrychowski, Katharina Huber and Steven Kelk. Worst-case optimal approximation algorithms for maximizing triplet consistency within phylogenetic networks. In Journal of Discrete Algorithms, Vol. 8(1):65-75, 2010.
Keywords: approximation, explicit network, from triplets, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/0710.3258.

Toggle abstract

@Article{BGHK2010,
AUTHOR = {Byrka, Jaroslaw and Gawrychowski, Pawel and Huber, Katharina and Kelk, Steven},
TITLE = {Worst-case optimal approximation algorithms for maximizing triplet consistency within phylogenetic networks},
YEAR = {2010},
JOURNAL = {Journal of Discrete Algorithms},
VOLUME = {8},
NUMBER = {1},
PAGES = {65-75},
URL = {http://dx.doi.org/10.1016/j.jda.2009.01.004},
NOTE = {http://arxiv.org/abs/0710.3258},
ANNOTE = {BIBUPDATE : 20080312},
KEYWORDS = {approximation, explicit network, from triplets, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction}
}

2

Zhi-Zhong Chen and Lusheng Wang. HybridNET: a tool for constructing hybridization networks. In BIO, Vol. 26(22):2912-2913, 2010.
Keywords: agreement forest, FPT, from rooted trees, hybridization, phylogenetic network, phylogeny, Program HybridNET, software.
Note: http://rnc.r.dendai.ac.jp/~chen/papers/note2.pdf.

Toggle abstract

@Article{ChenWang2010,
AUTHOR = {Chen, Zhi-Zhong and Wang, Lusheng},
TITLE = {HybridNET: a tool for constructing hybridization networks},
YEAR = {2010},
JOURNAL = {BIO},
VOLUME = {26},
NUMBER = {22},
PAGES = {2912-2913},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq548},
NOTE = {http://rnc.r.dendai.ac.jp/~chen/papers/note2.pdf},
KEYWORDS = {agreement forest, FPT, from rooted trees, hybridization, phylogenetic network, phylogeny, Program HybridNET, software}
}

3

Philippe Gambette. Méthodes combinatoires de reconstruction de réseaux phylogénétiques. PhD thesis, Université Montpellier 2, France, 2010.
Keywords: abstract network, characterization, circular split system, explicit network, FPT, from clusters, from triplets, integer linear programming, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, Program Dendroscope, pyramid, reconstruction, split network, weak hierarchy.
Note: http://tel.archives-ouvertes.fr/tel-00608342/en/.

@PhdThesis{Gambette2010,
AUTHOR = {Gambette, Philippe},
TITLE = {M{\~A}�thodes combinatoires de reconstruction de r{\~A}�seaux phylog{\~A}�n{\~A}�tiques},
YEAR = {2010},
SCHOOL = {Universit{\~A}� Montpellier 2, France},
URL = {http://tel.archives-ouvertes.fr/tel-00608342/en/},
NOTE = {http://tel.archives-ouvertes.fr/tel-00608342/en/},
KEYWORDS = {abstract network, characterization, circular split system, explicit network, FPT, from clusters, from triplets, integer linear programming, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, Program Dendroscope, pyramid, reconstruction, split network, weak hierarchy}
}

4

Changiz Eslahchi, Mahnaz Habibi, Reza Hassanzadeh and Ehsan Mottaghi. MC-Net: a method for the construction of phylogenetic networks based on the Monte-Carlo method. In BMCEB, Vol. 10:254, 2010.
Keywords: abstract network, circular split system, from distances, heuristic, phylogenetic network, Program MC-Net, Program SplitsTree, software, split, split network.
Note: http://dx.doi.org/10.1186/1471-2148-10-254.

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@Article{EHHM2010,
AUTHOR = {Eslahchi, Changiz and Habibi, Mahnaz and Hassanzadeh, Reza and Mottaghi, Ehsan},
TITLE = {MC-Net: a method for the construction of phylogenetic networks based on the Monte-Carlo method},
YEAR = {2010},
JOURNAL = {BMCEB},
VOLUME = {10},
PAGES = {254},
URL = {http://dx.doi.org/10.1186/1471-2148-10-254},
NOTE = {http://dx.doi.org/10.1186/1471-2148-10-254},
KEYWORDS = {abstract network, circular split system, from distances, heuristic, phylogenetic network, Program MC-Net, Program SplitsTree, software, split, split network}
}

5

Luay Nakhleh. A Metric on the Space of Reduced Phylogenetic Networks. In TCBB, Vol. 7(2), 2010.
Keywords: distance between networks, phylogenetic network, phylogeny.
Note: http://www.cs.rice.edu/~nakhleh/Papers/tcbb-Metric.pdf.

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@Article{Nakhleh2010,
AUTHOR = {Nakhleh, Luay},
TITLE = {A Metric on the Space of Reduced Phylogenetic Networks},
YEAR = {2010},
JOURNAL = {TCBB},
VOLUME = {7},
NUMBER = {2},
URL = {http://dx.doi.org/10.1109/TCBB.2009.2},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/tcbb-Metric.pdf},
ANNOTE = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2009.2},
KEYWORDS = {distance between networks, phylogenetic network, phylogeny}
}

6

Gabriel Cardona, Mercè Llabrés, Francesc Rosselló and Gabriel Valiente. Path lengths in tree-child time consistent hybridization networks. In Information Sciences, Vol. 180(3):366-383, 2010.
Keywords: distance between networks, phylogenetic network, phylogeny, time consistent network, tree-child network.
Note: http://arxiv.org/abs/0807.0087?context=cs.CE.

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@Article{CLRV2010b,
AUTHOR = {Cardona, Gabriel and Llabr{\~A}�s, Merc{\~A}� and Rossell{\~A}�, Francesc and Valiente, Gabriel},
TITLE = {Path lengths in tree-child time consistent hybridization networks},
YEAR = {2010},
JOURNAL = {Information Sciences},
VOLUME = {180},
NUMBER = {3},
PAGES = {366-383},
URL = {http://dx.doi.org/10.1016/j.ins.2009.09.013},
NOTE = {http://arxiv.org/abs/0807.0087?context=cs.CE},
ANNOTE = {BIBUPDATE : 20080725},
KEYWORDS = {distance between networks, phylogenetic network, phylogeny, time consistent network, tree-child network}
}

7

Johannes Fischer and Daniel H. Huson. New Common Ancestor Problems in Trees and Directed Acyclic Graphs. In IPL, Vol. 110(8-9):331-335, 2010.
Keywords: explicit network, phylogenetic network, polynomial.
Note: http://www-ab.informatik.uni-tuebingen.de/people/fischer/lsa.pdf.

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@Article{FischerHuson2010,
AUTHOR = {Fischer, Johannes and Huson, Daniel H.},
TITLE = {New Common Ancestor Problems in Trees and Directed Acyclic Graphs},
YEAR = {2010},
JOURNAL = {IPL},
VOLUME = {110},
NUMBER = {8-9},
PAGES = {331-335},
URL = {http://dx.doi.org/10.1016/j.ipl.2010.02.014},
NOTE = {http://www-ab.informatik.uni-tuebingen.de/people/fischer/lsa.pdf},
KEYWORDS = {explicit network, phylogenetic network, polynomial}
}

8

Stephen J. Willson. Regular Networks Can Be Uniquely Constructed from Their Trees. In TCBB, Vol. 8(3):785-796, 2010.
Keywords: explicit network, from rooted trees, phylogenetic network, phylogeny, reconstruction, regular network.
Note: http://www.public.iastate.edu/~swillson/RegularNetsFromTrees5.pdf.

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@Article{Willson2010,
AUTHOR = {Willson, Stephen J.},
TITLE = {Regular Networks Can Be Uniquely Constructed from Their Trees},
YEAR = {2010},
JOURNAL = {TCBB},
VOLUME = {8},
NUMBER = {3},
PAGES = {785-796},
URL = {http://dx.doi.org/10.1109/TCBB.2010.69},
NOTE = {http://www.public.iastate.edu/~swillson/RegularNetsFromTrees5.pdf},
KEYWORDS = {explicit network, from rooted trees, phylogenetic network, phylogeny, reconstruction, regular network}
}

9

Frederick A. Matsen. ConstNJ: an algorithm to reconstruct sets of phylogenetic trees satisfying pairwise topological constraints. In JCB, Vol. 17(6):799-818, 2010.
Keywords: from distances, Program constNJ, reconstruction.
Note: http://arxiv.org/abs/0901.1598v2.

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@Article{Matsen2010,
AUTHOR = {Matsen, Frederick A.},
TITLE = {ConstNJ: an algorithm to reconstruct sets of phylogenetic trees satisfying pairwise topological constraints},
YEAR = {2010},
JOURNAL = {JCB},
VOLUME = {17},
NUMBER = {6},
PAGES = {799-818},
URL = {http://dx.doi.org/10.1089/cmb.2009.0201},
NOTE = {http://arxiv.org/abs/0901.1598v2},
KEYWORDS = {from distances, Program constNJ, reconstruction}
}

10

Luay Nakhleh. Evolutionary phylogenetic networks: models and issues. In L. Heath and N. Ramakrishnan editors, The Problem Solving Handbook for Computational Biology and Bioinformatics, Springer, 2010.
Keywords: phylogenetic network, phylogeny, survey.
Note: http://www.cs.rice.edu/~nakhleh/Papers/HeathRamakrishnanBookChapter.pdf.

@InBook{Nakhleh2010b,
AUTHOR = {Nakhleh, Luay},
TITLE = {Evolutionary phylogenetic networks: models and issues},
YEAR = {2010},
BOOKTITLE = {The Problem Solving Handbook for Computational Biology and Bioinformatics},
EDITOR = {Heath, L. and Ramakrishnan, N.},
PUBLISHER = {Springer},
URL = {http://dx.doi.org/10.1007/978-0-387-09760-2_7},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/HeathRamakrishnanBookChapter.pdf},
KEYWORDS = {phylogenetic network, phylogeny, survey}
}

11

Stephen J. Willson. Properties of normal phylogenetic networks. In BMB, Vol. 72(2):340-358, 2010.
Keywords: normal network, phylogenetic network, phylogeny, regular network.
Note: http://www.public.iastate.edu/~swillson/RestrictionsOnNetworkspap9.pdf, slides available at http://www.newton.cam.ac.uk/webseminars/pg+ws/2007/plg/plgw01/0904/willson/.

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@Article{Willson2010b,
AUTHOR = {Willson, Stephen J.},
TITLE = {Properties of normal phylogenetic networks},
YEAR = {2010},
JOURNAL = {BMB},
VOLUME = {72},
NUMBER = {2},
PAGES = {340-358},
URL = {http://dx.doi.org/10.1007/s11538-009-9449-z},
NOTE = {http://www.public.iastate.edu/~swillson/RestrictionsOnNetworkspap9.pdf, slides available at http://www.newton.cam.ac.uk/webseminars/pg+ws/2007/plg/plgw01/0904/willson/},
KEYWORDS = {normal network, phylogenetic network, phylogeny, regular network}
}

12

Leo van Iersel, Steven Kelk, Regula Rupp and Daniel H. Huson. Phylogenetic Networks Do not Need to Be Complex: Using Fewer Reticulations to Represent Conflicting Clusters. In ISMB10, Vol. 26(12):i124-i131 of BIO, 2010.
Keywords: from clusters, level k phylogenetic network, Program Dendroscope, Program HybridInterleave, Program HybridNumber, reconstruction.
Note: http://dx.doi.org/10.1093/bioinformatics/btq202, with proofs: http://arxiv.org/abs/0910.3082.

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@InProceedings{IKRH2010,
AUTHOR = {van Iersel, Leo and Kelk, Steven and Rupp, Regula and Huson, Daniel H.},
TITLE = {Phylogenetic Networks Do not Need to Be Complex: Using Fewer Reticulations to Represent Conflicting Clusters},
YEAR = {2010},
BOOKTITLE = {ISMB10},
VOLUME = {26},
NUMBER = {12},
PAGES = {i124-i131},
SERIES = {BIO},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq202},
NOTE = {http://dx.doi.org/10.1093/bioinformatics/btq202, with proofs: http://arxiv.org/abs/0910.3082},
KEYWORDS = {from clusters, level k phylogenetic network, Program Dendroscope, Program HybridInterleave, Program HybridNumber, reconstruction}
}

13

Leo van Iersel, Charles Semple and Mike Steel. Quantifying the Extent of Lateral Gene Transfer Required to Avert a 'Genome of Eden'. In BMB, Vol. 72:1783–1798, 2010.
Note: http://www.win.tue.nl/~liersel/LGT.pdf.

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@Article{ISS2010,
AUTHOR = {van Iersel, Leo and Semple, Charles and Steel, Mike},
TITLE = {Quantifying the Extent of Lateral Gene Transfer Required to Avert a 'Genome of Eden'},
YEAR = {2010},
JOURNAL = {BMB},
VOLUME = {72},
PAGES = {1783{\^a}��1798},
URL = {http://dx.doi.org/10.1007/s11538-010-9506-7},
NOTE = {http://www.win.tue.nl/~liersel/LGT.pdf}
}

14

Gianluca Della Vedova, Riccardo Dondi, Tao Jiang, Giulio Pavesi, Yuri Pirola and Lusheng Wang. Beyond evolutionary trees. In Natural Computing, Vol. 9(2):421-435, 2010.
Note: http://dx.doi.org/10.1007/s11047-009-9156-6.

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@Article{VDJPPW2010,
AUTHOR = {Della Vedova, Gianluca and Dondi, Riccardo and Jiang, Tao and Pavesi, Giulio and Pirola, Yuri and Wang, Lusheng},
TITLE = {Beyond evolutionary trees},
YEAR = {2010},
JOURNAL = {Natural Computing},
VOLUME = {9},
NUMBER = {2},
PAGES = {421-435},
URL = {http://dx.doi.org/10.1007/s11047-009-9156-6},
NOTE = {http://dx.doi.org/10.1007/s11047-009-9156-6}
}

15

Joel Velasco and Elliott Sober. Testing for Treeness: Lateral Gene Transfer, Phylogenetic Inference, and Model Selection. In Biology and Philosophy, Vol. 25(4):675-687, 2010.
Keywords: explicit network, model selection, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: http://joelvelasco.net/Papers/velascosober-testingfortreeness.pdf.

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@Article{VelascoSober2010,
AUTHOR = {Velasco, Joel and Sober, Elliott},
TITLE = {Testing for Treeness: Lateral Gene Transfer, Phylogenetic Inference, and Model Selection},
YEAR = {2010},
JOURNAL = {Biology and Philosophy},
VOLUME = {25},
NUMBER = {4},
PAGES = {675-687},
URL = {http://dx.doi.org/10.1007/s10539-010-9222-6},
NOTE = {http://joelvelasco.net/Papers/velascosober-testingfortreeness.pdf},
KEYWORDS = {explicit network, model selection, phylogenetic network, phylogeny, reconstruction, statistical model}
}

16

David A. Morrison. Using data-display networks for exploratory data analysis in phylogenetic studies. In MBE, Vol. 27(5):1044-1057, 2010.
Keywords: abstract network, hybridization, NeighborNet, Program SplitsTree, recombination, split decomposition.
Note: http://dx.doi.org/10.1093/molbev/msp309.

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@Article{Morrison2010,
AUTHOR = {Morrison, David A.},
TITLE = {Using data-display networks for exploratory data analysis in phylogenetic studies},
YEAR = {2010},
JOURNAL = {MBE},
VOLUME = {27},
NUMBER = {5},
PAGES = {1044-1057},
URL = {http://dx.doi.org/10.1093/molbev/msp309},
NOTE = {http://dx.doi.org/10.1093/molbev/msp309},
KEYWORDS = {abstract network, hybridization, NeighborNet, Program SplitsTree, recombination, split decomposition}
}

17

Simone Linz, Charles Semple and Tanja Stadler. Analyzing and reconstructing reticulation networks under timing constraints. In JOMB, Vol. 61(5):715-737, 2010.
Keywords: explicit network, from rooted trees, hybridization, lateral gene transfer, NP complete, phylogenetic network, phylogeny, reconstruction, time consistent network.
Note: http://dx.doi.org/10.1007/s00285-009-0319-y..

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@Article{LSS2010,
AUTHOR = {Linz, Simone and Semple, Charles and Stadler, Tanja},
TITLE = {Analyzing and reconstructing reticulation networks under timing constraints},
YEAR = {2010},
JOURNAL = {JOMB},
VOLUME = {61},
NUMBER = {5},
PAGES = {715-737},
URL = {http://dx.doi.org/10.1007/s00285-009-0319-y},
NOTE = {http://dx.doi.org/10.1007/s00285-009-0319-y.},
KEYWORDS = {explicit network, from rooted trees, hybridization, lateral gene transfer, NP complete, phylogenetic network, phylogeny, reconstruction, time consistent network}
}

18

Alix Boc, Hervé Philippe and Vladimir Makarenkov. Inferring and Validating Horizontal Gene Transfer Events Using Bipartition Dissimilarity. In Systematic Biology, Vol. 59(2):195-211, 2010.
Note: http://www.info2.uqam.ca/~makarenv/makarenv/Artcile_SB_2010.pdf.

@Article{BPM2010,
AUTHOR = {Boc, Alix and Philippe, Herv{\~A}� and Makarenkov, Vladimir},
TITLE = {Inferring and Validating Horizontal Gene Transfer Events Using Bipartition Dissimilarity},
YEAR = {2010},
JOURNAL = {Systematic Biology},
VOLUME = {59},
NUMBER = {2},
PAGES = {195-211},
URL = {http://dx.doi.org/10.1093/sysbio/syp103},
NOTE = {http://www.info2.uqam.ca/~makarenv/makarenv/Artcile_SB_2010.pdf}
}

19

Tetsuo Asano, Jesper Jansson, Kunihiko Sadakane, Ryuhei Uehara and Gabriel Valiente. Faster Computation of the Robinson-Foulds Distance between Phylogenetic Networks. In CPM10, Vol. 6129:190-201 of LNCS, springer, 2010.
Keywords: distance between networks, explicit network, level k phylogenetic network, phylogenetic network, polynomial, spread.
Note: http://hdl.handle.net/10119/9859, slides available at http://cs.nyu.edu/parida/CPM2010/MainPage_files/18.pdf.

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@InProceedings{AJSUV2010,
AUTHOR = {Asano, Tetsuo and Jansson, Jesper and Sadakane, Kunihiko and Uehara, Ryuhei and Valiente, Gabriel},
TITLE = {Faster Computation of the Robinson-Foulds Distance between Phylogenetic Networks},
YEAR = {2010},
BOOKTITLE = {CPM10},
VOLUME = {6129},
PAGES = {190-201},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-642-13509-5_18},
NOTE = {http://hdl.handle.net/10119/9859, slides available at http://cs.nyu.edu/parida/CPM2010/MainPage_files/18.pdf},
KEYWORDS = {distance between networks, explicit network, level k phylogenetic network, phylogenetic network, polynomial, spread}
}

20

Erik W. Bloomquist and Marc A. Suchard. Unifying Vertical and Nonvertical Evolution: A Stochastic ARG-based Framework. In Systematic Biology, Vol. 59(1):27-41, 2010.
Note: http://dx.doi.org/10.1093/sysbio/syp076.

@Article{BloomquistSuchard2010,
AUTHOR = {Bloomquist, Erik W. and Suchard, Marc A.},
TITLE = {Unifying Vertical and Nonvertical Evolution: A Stochastic ARG-based Framework},
YEAR = {2010},
JOURNAL = {Systematic Biology},
VOLUME = {59},
NUMBER = {1},
PAGES = {27-41},
URL = {http://dx.doi.org/10.1093/sysbio/syp076},
NOTE = {http://dx.doi.org/10.1093/sysbio/syp076}
}

21

Yufeng Wu. Close Lower and Upper Bounds for the Minimum Reticulate Network of Multiple Phylogenetic Trees. In ISMB10, Vol. 26(12):i140-i148 of BIO, 2010.
Keywords: explicit network, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program PIRN, software.
Note: http://dx.doi.org/10.1093/bioinformatics/btq198.

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@InProceedings{Wu2010,
AUTHOR = {Wu, Yufeng},
TITLE = {Close Lower and Upper Bounds for the Minimum Reticulate Network of Multiple Phylogenetic Trees},
YEAR = {2010},
BOOKTITLE = {ISMB10},
VOLUME = {26},
NUMBER = {12},
PAGES = {i140-i148},
SERIES = {BIO},
URL = {http://dx.doi.org/10.1093/bioinformatics/btq198},
NOTE = {http://dx.doi.org/10.1093/bioinformatics/btq198},
KEYWORDS = {explicit network, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program PIRN, software}
}

22

Yufeng Wu and Jiayin Wang. Fast Computation of the Exact Hybridization Number of Two Phylogenetic Trees. In ISBRA10, Vol. 6053:203-214 of LNCS, springer, 2010.
Keywords: agreement forest, explicit network, from rooted trees, hybridization, integer linear programming, minimum number, phylogenetic network, phylogeny, Program HybridNumber, Program SPRDist, SPR distance.
Note: http://www.engr.uconn.edu/~ywu/Papers/ISBRA10WuWang.pdf.

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@InProceedings{WuWang2010,
AUTHOR = {Wu, Yufeng and Wang, Jiayin},
TITLE = {Fast Computation of the Exact Hybridization Number of Two Phylogenetic Trees},
YEAR = {2010},
BOOKTITLE = {ISBRA10},
VOLUME = {6053},
PAGES = {203-214},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-642-13078-6_23},
NOTE = {http://www.engr.uconn.edu/~ywu/Papers/ISBRA10WuWang.pdf},
KEYWORDS = {agreement forest, explicit network, from rooted trees, hybridization, integer linear programming, minimum number, phylogenetic network, phylogeny, Program HybridNumber, Program SPRDist, SPR distance}
}

23

Robert G. Beiko. Gene sharing and genome evolution: networks in trees and trees in networks. In Biology and Philosophy, Vol. 25(4):659-673, 2010.
Keywords: abstract network, explicit network, from rooted trees, galled network, phylogenetic network, phylogeny, Program Dendroscope, Program SplitsTree, reconstruction, split network, survey.
Note: http://dx.doi.org/10.1007/s10539-010-9217-3.

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@Article{Beiko2010,
AUTHOR = {Beiko, Robert G.},
TITLE = {Gene sharing and genome evolution: networks in trees and trees in networks},
YEAR = {2010},
JOURNAL = {Biology and Philosophy},
VOLUME = {25},
NUMBER = {4},
PAGES = {659-673},
URL = {http://dx.doi.org/10.1007/s10539-010-9217-3},
NOTE = {http://dx.doi.org/10.1007/s10539-010-9217-3},
KEYWORDS = {abstract network, explicit network, from rooted trees, galled network, phylogenetic network, phylogeny, Program Dendroscope, Program SplitsTree, reconstruction, split network, survey}
}

24

Miguel Arenas, Mateus Patricio, David Posada and Gabriel Valiente. Characterization of Phylogenetic Networks with NetTest. In BMCB, Vol. 11:268, 2010.
Keywords: explicit network, galled tree, phylogenetic network, Program NetTest, software, time consistent network, tree sibling network, tree-child network, visualization.
Note: http://dx.doi.org/10.1186/1471-2105-11-268, software available at http://darwin.uvigo.es/software/nettest/.

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@Article{APPV2010,
AUTHOR = {Arenas, Miguel and Patricio, Mateus and Posada, David and Valiente, Gabriel},
TITLE = {Characterization of Phylogenetic Networks with NetTest},
YEAR = {2010},
JOURNAL = {BMCB},
VOLUME = {11},
PAGES = {268},
URL = {http://dx.doi.org/10.1186/1471-2105-11-268},
NOTE = {http://dx.doi.org/10.1186/1471-2105-11-268, software available at http://darwin.uvigo.es/software/nettest/},
KEYWORDS = {explicit network, galled tree, phylogenetic network, Program NetTest, software, time consistent network, tree sibling network, tree-child network, visualization}
}

25

David A. Morrison. Phylogenetic networks in systematic biology (and elsewhere) In R.M. Mohan editor, Research Advances in Systematic Biology, Global Research Network, Trivandrum, India, 2010.
Keywords: abstract network, explicit network, phylogenetic network, phylogeny, reconstruction, survey.

@InBook{Morrison2010b,
AUTHOR = {Morrison, David A.},
TITLE = {Phylogenetic networks in systematic biology (and elsewhere)},
YEAR = {2010},
BOOKTITLE = {Research Advances in Systematic Biology},
EDITOR = {Mohan, R.M.},
PUBLISHER = {Global Research Network, Trivandrum, India},
KEYWORDS = {abstract network, explicit network, phylogenetic network, phylogeny, reconstruction, survey}
}

26

Hyun Jung Park, Guohua Jin and Luay Nakhleh. Bootstrap-based Support of HGT Inferred by Maximum Parsimony. In BMCEB, Vol. 10:131, 2010.
Keywords: bootstrap, explicit network, from sequences, lateral gene transfer, parsimony, phylogenetic network, phylogeny, Program Nepal, reconstruction.
Note: http://dx.doi.org/10.1186/1471-2148-10-131.

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@Article{PJN2010,
AUTHOR = {Park, Hyun Jung and Jin, Guohua and Nakhleh, Luay},
TITLE = {Bootstrap-based Support of HGT Inferred by Maximum Parsimony},
YEAR = {2010},
JOURNAL = {BMCEB},
VOLUME = {10},
PAGES = {131},
URL = {http://dx.doi.org/10.1186/1471-2148-10-131},
NOTE = {http://dx.doi.org/10.1186/1471-2148-10-131},
KEYWORDS = {bootstrap, explicit network, from sequences, lateral gene transfer, parsimony, phylogenetic network, phylogeny, Program Nepal, reconstruction}
}

27

Leo van Iersel, Charles Semple and Mike Steel. Locating a tree in a phylogenetic network. In IPL, Vol. 110(23), 2010.
Keywords: cluster containment, explicit network, from network, level k phylogenetic network, normal network, NP complete, phylogenetic network, polynomial, regular network, time consistent network, tree containment, tree sibling network, tree-child network.
Note: http://arxiv.org/abs/1006.3122.

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@Article{ISS2010b,
AUTHOR = {van Iersel, Leo and Semple, Charles and Steel, Mike},
TITLE = {Locating a tree in a phylogenetic network},
YEAR = {2010},
JOURNAL = {IPL},
VOLUME = {110},
NUMBER = {23},
URL = {http://dx.doi.org/10.1016/j.ipl.2010.07.027},
NOTE = {http://arxiv.org/abs/1006.3122},
KEYWORDS = {cluster containment, explicit network, from network, level k phylogenetic network, normal network, NP complete, phylogenetic network, polynomial, regular network, time consistent network, tree containment, tree sibling network, tree-child network}
}

28

Sophie Abby, Eric Tannier, Manolo Gouy and Vincent Daubin. Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests. In BMCB, Vol. 11:324, 2010.
Keywords: agreement forest, explicit network, from rooted trees, from species tree, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program EEEP, Program PhyloNet, Program Prunier, reconstruction, software.
Note: http://www.biomedcentral.com/1471-2105/11/324.

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@Article{ATGD2010,
AUTHOR = {Abby, Sophie and Tannier, Eric and Gouy, Manolo and Daubin, Vincent},
TITLE = {Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests},
YEAR = {2010},
JOURNAL = {BMCB},
VOLUME = {11},
PAGES = {324},
URL = {http://dx.doi.org/10.1186/1471-2105-11-324},
NOTE = {http://www.biomedcentral.com/1471-2105/11/324},
KEYWORDS = {agreement forest, explicit network, from rooted trees, from species tree, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program EEEP, Program PhyloNet, Program Prunier, reconstruction, software}
}

29

Hyun Jung Park, Guohua Jin and Luay Nakhleh. Algorithmic strategies for estimating the amount of reticulation from a collection of gene trees. In CSB10, 2010.
Keywords: bound, from rooted trees, heuristic, phylogenetic network, phylogeny, reconstruction, SPR distance.
Note: http://www.cs.rice.edu/~nakhleh/Papers/ParkEtAl-CSB2010.pdf.

@InProceedings{PJN2010b,
AUTHOR = {Park, Hyun Jung and Jin, Guohua and Nakhleh, Luay},
TITLE = {Algorithmic strategies for estimating the amount of reticulation from a collection of gene trees},
YEAR = {2010},
BOOKTITLE = {CSB10},
URL = {http://www.lifesciencessociety.org/CSB2010/toc/PDF/114.2010.pdf},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/ParkEtAl-CSB2010.pdf},
KEYWORDS = {bound, from rooted trees, heuristic, phylogenetic network, phylogeny, reconstruction, SPR distance}
}

30

Gabriel Cardona, Mercè Llabrés and Francesc Rosselló. A metric for galled networks. 2010.
Keywords: distance between networks, explicit network, from network, galled network, phylogenetic network, phylogeny.
Note: http://arxiv4.library.cornell.edu/abs/1009.0652.

@Misc{CMF2010,
AUTHOR = {Cardona, Gabriel and Llabr{\~A}�s, Merc{\~A}� and Rossell{\~A}�, Francesc},
TITLE = {A metric for galled networks},
YEAR = {2010},
NOTE = {http://arxiv4.library.cornell.edu/abs/1009.0652},
KEYWORDS = {distance between networks, explicit network, from network, galled network, phylogenetic network, phylogeny}
}

31

Chris Whidden, Robert G. Beiko and Norbert Zeh. Fast FPT Algorithms for Computing Rooted Agreement Forests: Theory and Experiments. In Proceedings of the ninth International Symposium on Experimental Algorithms (SEA'10), Vol. 6049:141-153 of LNCS, springer, 2010.
Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, SPR distance.
Note: https://www.cs.dal.ca/sites/default/files/technical_reports/CS-2010-03.pdf.

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@InProceedings{WBZ2010,
AUTHOR = {Whidden, Chris and Beiko, Robert G. and Zeh, Norbert},
TITLE = {Fast FPT Algorithms for Computing Rooted Agreement Forests: Theory and Experiments},
YEAR = {2010},
BOOKTITLE = {Proceedings of the ninth International Symposium on Experimental Algorithms (SEA'10)},
VOLUME = {6049},
PAGES = {141-153},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-642-13193-6_13},
NOTE = {https://www.cs.dal.ca/sites/default/files/technical_reports/CS-2010-03.pdf},
KEYWORDS = {agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, SPR distance}
}

32

Fumei Lam, Ryan Tarpine and Sorin Istrail. The Imperfect Ancestral Recombination Graph Reconstruction Problem: Upper Bounds for Recombination and Homoplasy. In JCB, Vol. 17(6), 2010.
Keywords: explicit network, from sequences, heuristic, phylogenetic network, phylogeny, reconstruction.
Note: http://www.cs.brown.edu/~sorin/pdfs/Lam%20the%20imperfect.pdf.

@Article{LTI2010,
AUTHOR = {Lam, Fumei and Tarpine, Ryan and Istrail, Sorin},
TITLE = {The Imperfect Ancestral Recombination Graph Reconstruction Problem: Upper Bounds for Recombination and Homoplasy},
YEAR = {2010},
JOURNAL = {JCB},
VOLUME = {17},
NUMBER = {6},
URL = {http://dx.doi.org/10.1089/cmb.2009.024},
NOTE = {http://www.cs.brown.edu/~sorin/pdfs/Lam%20the%20imperfect.pdf},
KEYWORDS = {explicit network, from sequences, heuristic, phylogenetic network, phylogeny, reconstruction}
}

33

Gabriel Cardona, Mercè Llabrés and Francesc Rosselló. Two Results on Distances for Phylogenetic Networks. In Advances in Intelligent and Soft Computing, Vol. 74:93-100, 2010.
Keywords: distance between networks, explicit network, phylogenetic network, phylogeny, tree sibling network.
Note: http://www.merilibrary.com/books/bioinformatics/advances%20in%20bioinformatics.pdf#page=103.

@Article{CLR2010b,
AUTHOR = {Cardona, Gabriel and Llabr{\~A}�s, Merc{\~A}� and Rossell{\~A}�, Francesc},
TITLE = {Two Results on Distances for Phylogenetic Networks},
YEAR = {2010},
JOURNAL = {Advances in Intelligent and Soft Computing},
VOLUME = {74},
PAGES = {93-100},
URL = {http://dx.doi.org/10.1007/978-3-642-13214-8_12},
NOTE = {http://www.merilibrary.com/books/bioinformatics/advances%20in%20bioinformatics.pdf#page=103},
KEYWORDS = {distance between networks, explicit network, phylogenetic network, phylogeny, tree sibling network}
}

34

Cuong Than. Inference of parsimonious species phylogenies from multi-locus data. PhD thesis, Rice University, U.S.A., 2010.
Keywords: explicit network, from sequences, parsimony, phylogenetic network, phylogeny, reconstruction.
Note: http://hdl.handle.net/1911/62177.

@PhdThesis{Than2010,
AUTHOR = {Than, Cuong},
TITLE = {Inference of parsimonious species phylogenies from multi-locus data},
YEAR = {2010},
SCHOOL = {Rice University, U.S.A.},
NOTE = {http://hdl.handle.net/1911/62177},
KEYWORDS = {explicit network, from sequences, parsimony, phylogenetic network, phylogeny, reconstruction}
}

35

Marta Melé, Asif Javed, Marc Pybus, Francesc Calafell, Laxmi Parida, Jaume Bertranpetit and Genographic Consortium. A New Method to Reconstruct Recombination Events at a Genomic Scale. In PLoS Computational Biology, Vol. 6(11):e1001010.1-13, 2010.
Keywords: explicit network, from sequences, phylogenetic network, phylogeny.
Note: http://dx.doi.org/10.1371/journal.pcbi.1001010.

Toggle abstract

@Article{MJPCPBC2010,
AUTHOR = {Mel{\~A}�, Marta and Javed, Asif and Pybus, Marc and Calafell, Francesc and Parida, Laxmi and Bertranpetit, Jaume and Consortium, Genographic},
TITLE = {A New Method to Reconstruct Recombination Events at a Genomic Scale},
YEAR = {2010},
JOURNAL = {PLoS Computational Biology},
VOLUME = {6},
NUMBER = {11},
PAGES = {e1001010.1-13},
URL = {http://dx.doi.org/10.1371/journal.pcbi.1001010},
NOTE = {http://dx.doi.org/10.1371/journal.pcbi.1001010},
KEYWORDS = {explicit network, from sequences, phylogenetic network, phylogeny}
}

36

Sagi Snir and Edward Trifonov. A Novel Technique for Detecting Putative Horizontal Gene Transfer in the Sequence Space. In JCB, Vol. 17(11):1535-1548, 2010.
Keywords: from sequences, phylogenetic network, phylogeny, reconstruction.
Note: http://research.haifa.ac.il/~ssagi/published%20papers/JCB-HGT.pdf.

Toggle abstract

@Article{SnirTrifonov2010,
AUTHOR = {Snir, Sagi and Trifonov, Edward},
TITLE = {A Novel Technique for Detecting Putative Horizontal Gene Transfer in the Sequence Space},
YEAR = {2010},
JOURNAL = {JCB},
VOLUME = {17},
NUMBER = {11},
PAGES = {1535-1548},
URL = {http://dx.doi.org/10.1089/cmb.2010.0095},
NOTE = {http://research.haifa.ac.il/~ssagi/published%20papers/JCB-HGT.pdf},
KEYWORDS = {from sequences, phylogenetic network, phylogeny, reconstruction}
}

37

Binh T. Nguyen. Novel Split-Based Approaches to Computing Phylogenetic Diversity and Planar Split Networks. PhD thesis, University of East Anglia, U.K., 2010.
Keywords: abstract network, diversity, from splits, phylogenetic network, phylogeny, reconstruction, split, split network, visualization.
Note: https://ueaeprints.uea.ac.uk/id/eprint/34218.

@PhdThesis{Nguyen2010,
AUTHOR = {Nguyen, Binh T.},
TITLE = {Novel Split-Based Approaches to Computing Phylogenetic Diversity and Planar Split Networks},
YEAR = {2010},
SCHOOL = {University of East Anglia, U.K.},
NOTE = {https://ueaeprints.uea.ac.uk/id/eprint/34218},
KEYWORDS = {abstract network, diversity, from splits, phylogenetic network, phylogeny, reconstruction, split, split network, visualization}
}

38

Pawel Górecki. H-trees: a model of evolutionary scenario with horizontal gene transfer. In Fundamenta Informaticae, Vol. 103:105-128, 2010.
Keywords: duplication, lateral gene transfer, loss, phylogenetic network, phylogeny, uniqueness.

@Article{Gorecki2010,
AUTHOR = {G{\~A}�recki, Pawel},
TITLE = {H-trees: a model of evolutionary scenario with horizontal gene transfer},
YEAR = {2010},
JOURNAL = {Fundamenta Informaticae},
VOLUME = {103},
PAGES = {105-128},
URL = {http://dx.doi.org/10.3233/FI-2010-321},
KEYWORDS = {duplication, lateral gene transfer, loss, phylogenetic network, phylogeny, uniqueness}
}

2009

1

Gabriel Cardona, Francesc Rosselló and Gabriel Valiente. Comparison of tree-child phylogenetic networks. In TCBB, Vol. 6(4):552-569, 2009.
Keywords: explicit network, phylogenetic network, phylogeny, Program Bio PhyloNetwork, Program PhyloNetwork, tree sibling network, tree-child network.
Note: http://arxiv.org/abs/0708.3499.

Toggle abstract

@Article{CRV2009,
AUTHOR = {Cardona, Gabriel and Rossell{\~A}�, Francesc and Valiente, Gabriel},
TITLE = {Comparison of tree-child phylogenetic networks},
YEAR = {2009},
JOURNAL = {TCBB},
VOLUME = {6},
NUMBER = {4},
PAGES = {552-569},
URL = {http://dx.doi.org/10.1109/TCBB.2007.70270},
NOTE = {http://arxiv.org/abs/0708.3499},
ANNOTE = {BIBUPDATE : 20070924},
KEYWORDS = {explicit network, phylogenetic network, phylogeny, Program Bio PhyloNetwork, Program PhyloNetwork, tree sibling network, tree-child network}
}

2

Stefan Grünewald, Vincent Moulton and Andreas Spillner. Consistency of the QNet algorithm for generating planar split networks from weighted quartets. In DAM, Vol. 157(10):2325-2334, 2009.
Keywords: abstract network, consistency, from quartets, phylogenetic network, phylogeny, Program QNet, reconstruction, software.
Note: http://dx.doi.org/10.1016/j.dam.2008.06.038.

Toggle abstract

@Article{GMS2009,
AUTHOR = {Gr{\~A}�newald, Stefan and Moulton, Vincent and Spillner, Andreas},
TITLE = {Consistency of the QNet algorithm for generating planar split networks from weighted quartets},
YEAR = {2009},
JOURNAL = {DAM},
VOLUME = {157},
NUMBER = {10},
PAGES = {2325-2334},
URL = {http://dx.doi.org/10.1016/j.dam.2008.06.038},
NOTE = {http://dx.doi.org/10.1016/j.dam.2008.06.038},
ANNOTE = {CITE : },
KEYWORDS = {abstract network, consistency, from quartets, phylogenetic network, phylogeny, Program QNet, reconstruction, software}
}

3

Ulrik Brandes and Sabine Cornelsen. Phylogenetic Graph Models Beyond Trees. In DAM, Vol. 157(10):2361-2369, 2009.
Keywords: abstract network, cactus graph, from splits, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.inf.uni-konstanz.de/~cornelse/Papers/bc-pgmbt-07.pdf.

Toggle abstract

@Article{BrandesCornelsen2009,
AUTHOR = {Brandes, Ulrik and Cornelsen, Sabine},
TITLE = {Phylogenetic Graph Models Beyond Trees},
YEAR = {2009},
JOURNAL = {DAM},
VOLUME = {157},
NUMBER = {10},
PAGES = {2361-2369},
URL = {http://dx.doi.org/10.1016/j.dam.2008.06.031},
NOTE = {http://www.inf.uni-konstanz.de/~cornelse/Papers/bc-pgmbt-07.pdf},
KEYWORDS = {abstract network, cactus graph, from splits, phylogenetic network, phylogeny, polynomial, reconstruction}
}

4

Leo van Iersel, Steven Kelk and Matthias Mnich. Uniqueness, intractability and exact algorithms: reflections on level-k phylogenetic networks. In JBCB, Vol. 7(4):597-623, 2009.
Keywords: explicit network, from triplets, galled tree, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: http://arxiv.org/pdf/0712.2932v2.

@Article{IKM2009,
AUTHOR = {van Iersel, Leo and Kelk, Steven and Mnich, Matthias},
TITLE = {Uniqueness, intractability and exact algorithms: reflections on level-k phylogenetic networks},
YEAR = {2009},
JOURNAL = {JBCB},
VOLUME = {7},
NUMBER = {4},
PAGES = {597-623},
URL = {http://dx.doi.org/10.1142/S0219720009004308},
NOTE = {http://arxiv.org/pdf/0712.2932v2},
ANNOTE = {BIBUPDATE : 20081216},
KEYWORDS = {explicit network, from triplets, galled tree, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, reconstruction, uniqueness}
}

5

Daniel H. Huson. Drawing Rooted Phylogenetic Networks. In TCBB, Vol. 6(1):103-109, 2009.
Keywords: explicit network, phylogenetic network, phylogeny, Program Dendroscope, Program SplitsTree, visualization.
Note: http://dx.doi.org/10.1109/TCBB.2008.58.

Toggle abstract

@Article{Huson2009,
AUTHOR = {Huson, Daniel H.},
TITLE = {Drawing Rooted Phylogenetic Networks},
YEAR = {2009},
JOURNAL = {TCBB},
VOLUME = {6},
NUMBER = {1},
PAGES = {103-109},
URL = {http://dx.doi.org/10.1109/TCBB.2008.58},
NOTE = {http://dx.doi.org/10.1109/TCBB.2008.58},
ANNOTE = {CITE : },
KEYWORDS = {explicit network, phylogenetic network, phylogeny, Program Dendroscope, Program SplitsTree, visualization}
}

6

Simone Linz and Charles Semple. Hybridization in non-binary trees. In TCBB, Vol. 6(1):30-45, 2009.
Keywords: agreement forest, FPT, from rooted trees, hybridization, phylogenetic network, phylogeny, reconstruction.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/LS08.pdf, slides available at http://www.newton.cam.ac.uk/webseminars/pg+ws/2007/plg/plgw03/1220/linz/.

@Article{LinzSemple2009,
AUTHOR = {Linz, Simone and Semple, Charles},
TITLE = {Hybridization in non-binary trees},
YEAR = {2009},
JOURNAL = {TCBB},
VOLUME = {6},
NUMBER = {1},
PAGES = {30-45},
URL = {http://dx.doi.org/10.1109/TCBB.2008.86},
NOTE = {http://www.math.canterbury.ac.nz/~c.semple/papers/LS08.pdf, slides available at http://www.newton.cam.ac.uk/webseminars/pg+ws/2007/plg/plgw03/1220/linz/},
ANNOTE = {CITE : },
KEYWORDS = {agreement forest, FPT, from rooted trees, hybridization, phylogenetic network, phylogeny, reconstruction}
}

7

Sagi Snir and Tamir Tuller. The NET-HMM approach: Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. In JBCB, Vol. 7(4):625-644, 2009.
Keywords: explicit network, from sequences, HMM, lateral gene transfer, likelihood, phylogenetic network, phylogeny, statistical model.
Note: http://research.haifa.ac.il/~ssagi/published%20papers/Snir-NET-HMM-JBCB-2009.pdf.

Toggle abstract

@Article{SnirTuller2009,
AUTHOR = {Snir, Sagi and Tuller, Tamir},
TITLE = {The NET-HMM approach: Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models},
YEAR = {2009},
JOURNAL = {JBCB},
VOLUME = {7},
NUMBER = {4},
PAGES = {625-644},
URL = {http://dx.doi.org/10.1142/S021972000900428X},
NOTE = {http://research.haifa.ac.il/~ssagi/published%20papers/Snir-NET-HMM-JBCB-2009.pdf},
ANNOTE = {CITE : },
KEYWORDS = {explicit network, from sequences, HMM, lateral gene transfer, likelihood, phylogenetic network, phylogeny, statistical model}
}

8

Stefan Grünewald, Katharina Huber, Vincent Moulton, Charles Semple and Andreas Spillner. Characterizing weak compatibility in terms of weighted quartets. In Advances in Applied Mathematics, Vol. 42(3):329-341, 2009.
Keywords: abstract network, characterization, from quartets, split network, weak hierarchy.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/GHMSS08.pdf, slides at http://www.lirmm.fr/miep08/slides/12_02_huber.pdf.

@Article{GHMSS2009,
AUTHOR = {Gr{\~A}�newald, Stefan and Huber, Katharina and Moulton, Vincent and Semple, Charles and Spillner, Andreas},
TITLE = {Characterizing weak compatibility in terms of weighted quartets},
YEAR = {2009},
JOURNAL = {Advances in Applied Mathematics},
VOLUME = {42},
NUMBER = {3},
PAGES = {329-341},
URL = {http://dx.doi.org/10.1016/j.aam.2008.07.002},
NOTE = {http://www.math.canterbury.ac.nz/~c.semple/papers/GHMSS08.pdf, slides at http://www.lirmm.fr/miep08/slides/12_02_huber.pdf},
ANNOTE = {BIBUPDATE : 20080722},
KEYWORDS = {abstract network, characterization, from quartets, split network, weak hierarchy}
}

9

Gabriel Cardona, Mercè Llabrés, Francesc Rosselló and Gabriel Valiente. Metrics for phylogenetic networks I: Generalizations of the Robinson-Foulds metric. In TCBB, Vol. 6(1):46-61, 2009.
Keywords: distance between networks, explicit network, phylogenetic network, phylogeny, time consistent network, tree-child network, tripartition distance.
Note: http://dx.doi.org/10.1109/TCBB.2008.70.

Toggle abstract

@Article{CLRV2009a,
AUTHOR = {Cardona, Gabriel and Llabr{\~A}�s, Merc{\~A}� and Rossell{\~A}�, Francesc and Valiente, Gabriel},
TITLE = {Metrics for phylogenetic networks I: Generalizations of the Robinson-Foulds metric},
YEAR = {2009},
JOURNAL = {TCBB},
VOLUME = {6},
NUMBER = {1},
PAGES = {46-61},
URL = {http://dx.doi.org/10.1109/TCBB.2008.70},
NOTE = {http://dx.doi.org/10.1109/TCBB.2008.70},
ANNOTE = {BIBUPDATE : 20080725},
KEYWORDS = {distance between networks, explicit network, phylogenetic network, phylogeny, time consistent network, tree-child network, tripartition distance}
}

10

Gabriel Cardona, Mercè Llabrés, Francesc Rosselló and Gabriel Valiente. Metrics for phylogenetic networks II: Nodal and triplets metrics. In TCBB, Vol. 6(3):454-469, 2009.
Keywords: distance between networks, phylogenetic network, phylogeny.
Note: http://dx.doi.org/10.1109/TCBB.2008.127.

Toggle abstract

@Article{CLRV2009b,
AUTHOR = {Cardona, Gabriel and Llabr{\~A}�s, Merc{\~A}� and Rossell{\~A}�, Francesc and Valiente, Gabriel},
TITLE = {Metrics for phylogenetic networks II: Nodal and triplets metrics},
YEAR = {2009},
JOURNAL = {TCBB},
VOLUME = {6},
NUMBER = {3},
PAGES = {454-469},
URL = {http://dx.doi.org/10.1109/TCBB.2008.127},
NOTE = {http://dx.doi.org/10.1109/TCBB.2008.127},
ANNOTE = {BIBUPDATE : 20080725},
KEYWORDS = {distance between networks, phylogenetic network, phylogeny}
}

11

Gabriel Cardona, Mercè Llabrés, Francesc Rosselló and Gabriel Valiente. On Nakhleh's metric for reduced phylogenetic networks. In TCBB, Vol. 6(4):629-638, 2009.
Keywords: distance between networks, phylogenetic network, phylogeny.
Note: Preliminary versions: http://arxiv.org/abs/0809.0110 and http://arxiv.org/abs/0801.2354v1.

Toggle abstract

@Article{CLRV2009d,
AUTHOR = {Cardona, Gabriel and Llabr{\~A}�s, Merc{\~A}� and Rossell{\~A}�, Francesc and Valiente, Gabriel},
TITLE = {On Nakhleh's metric for reduced phylogenetic networks},
YEAR = {2009},
JOURNAL = {TCBB},
VOLUME = {6},
NUMBER = {4},
PAGES = {629-638},
URL = {http://dx.doi.org/10.1109/TCBB.2009.33},
NOTE = {Preliminary versions: http://arxiv.org/abs/0809.0110 and http://arxiv.org/abs/0801.2354v1},
ANNOTE = {BIBUPDATE : 20080925},
KEYWORDS = {distance between networks, phylogenetic network, phylogeny}
}

12

Guohua Jin, Luay Nakhleh, Sagi Snir and Tamir Tuller. Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-time Heuristic. In TCBB, Vol. 6(3):495-505, 2009.
Keywords: explicit network, heuristic, parsimony, phylogenetic network, phylogeny, reconstruction.
Note: http://www.cs.rice.edu/~nakhleh/Papers/tcbb-MP.pdf.

@Article{JNST2009,
AUTHOR = {Jin, Guohua and Nakhleh, Luay and Snir, Sagi and Tuller, Tamir},
TITLE = {Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-time Heuristic},
YEAR = {2009},
JOURNAL = {TCBB},
VOLUME = {6},
NUMBER = {3},
PAGES = {495-505},
URL = {http://dx.doi.org/10.1109/TCBB.2008.119},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/tcbb-MP.pdf},
ANNOTE = {BIBUPDATE : 20081028},
KEYWORDS = {explicit network, heuristic, parsimony, phylogenetic network, phylogeny, reconstruction}
}

13

Luay Nakhleh, Derek Ruths and Hideki Innan. Gene Trees, Species Trees, and Species Networks. In R. Guerra, D. B. Allison and D. Goldstein editors, Meta-analysis and Combining Information in Genetics and Genomics, 2009.
Keywords: coalescent, explicit network, from rooted trees, from species tree, phylogenetic network, phylogeny, reconstruction.
Note: http://www.cs.rice.edu/~nakhleh/Papers/GuerraGoldsteinBookChapter.pdf.

@InBook{NRI2009,
AUTHOR = {Nakhleh, Luay and Ruths, Derek and Innan, Hideki},
TITLE = {Gene Trees, Species Trees, and Species Networks},
YEAR = {2009},
BOOKTITLE = {Meta-analysis and Combining Information in Genetics and Genomics},
EDITOR = {Guerra, R. and Allison, D. B. and Goldstein, D.},
URL = {http://dx.doi.org/10.1201/9781420010626.ch17},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/GuerraGoldsteinBookChapter.pdf},
ANNOTE = {BIBUPDATE : 20081127 http://www.cs.rice.edu/~nakhleh/Papers/NakhlehRuthsInnan.pdf},
KEYWORDS = {coalescent, explicit network, from rooted trees, from species tree, phylogenetic network, phylogeny, reconstruction}
}

14

Leo van Iersel. Algorithms, Haplotypes and Phylogenetic Networks. PhD thesis, Eindhoven University of Technology, The Netherlands, 2009.
Keywords: evaluation, explicit network, exponential algorithm, FPT, from triplets, galled tree, level k phylogenetic network, mu distance, phylogenetic network, phylogeny, polynomial, Program Level2, Program Marlon, Program Simplistic, Program T REX, reconstruction.
Note: http://www.win.tue.nl/~liersel/thesis_vaniersel_viewing.pdf.

@PhdThesis{Iersel2009,
AUTHOR = {van Iersel, Leo},
TITLE = {Algorithms, Haplotypes and Phylogenetic Networks},
YEAR = {2009},
SCHOOL = {Eindhoven University of Technology, The Netherlands},
NOTE = {http://www.win.tue.nl/~liersel/thesis_vaniersel_viewing.pdf},
ANNOTE = {CITE : },
KEYWORDS = {evaluation, explicit network, exponential algorithm, FPT, from triplets, galled tree, level k phylogenetic network, mu distance, phylogenetic network, phylogeny, polynomial, Program Level2, Program Marlon, Program Simplistic, Program T REX, reconstruction}
}

15

Ran Libeskind-Hadas and Michael A. Charleston. On the Computational Complexity of the Reticulate Cophylogeny Reconstruction Problem. In JCB, Vol. 16(1):105-117, 2009.
Keywords: cophylogeny, heuristic, NP complete, parsimony, phylogenetic network, reconstruction.
Note: http://dx.doi.org/10.1089/cmb.2008.0084.

Toggle abstract

@Article{LiebeskindCharleston2009,
AUTHOR = {Libeskind-Hadas, Ran and Charleston, Michael A.},
TITLE = {On the Computational Complexity of the Reticulate Cophylogeny Reconstruction Problem},
YEAR = {2009},
JOURNAL = {JCB},
VOLUME = {16},
NUMBER = {1},
PAGES = {105-117},
URL = {http://dx.doi.org/10.1089/cmb.2008.0084},
NOTE = {http://dx.doi.org/10.1089/cmb.2008.0084},
ANNOTE = {BIBUPDATE : 20090105},
KEYWORDS = {cophylogeny, heuristic, NP complete, parsimony, phylogenetic network, reconstruction}
}

16

Thu-Hien To and Michel Habib. Level-k Phylogenetic Networks Are Constructable from a Dense Triplet Set in Polynomial Time. In CPM09, (5577):275-288, springer, 2009.
Keywords: explicit network, from triplets, level k phylogenetic network, minimum number, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://arxiv.org/abs/0901.1657.

Toggle abstract

@InProceedings{ToHabib2009,
AUTHOR = {To, Thu-Hien and Habib, Michel},
TITLE = {Level-k Phylogenetic Networks Are Constructable from a Dense Triplet Set in Polynomial Time},
YEAR = {2009},
BOOKTITLE = {CPM09},
NUMBER = {5577},
PAGES = {275-288},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-642-02441-2_25},
NOTE = {http://arxiv.org/abs/0901.1657},
KEYWORDS = {explicit network, from triplets, level k phylogenetic network, minimum number, phylogenetic network, phylogeny, polynomial, reconstruction}
}

17

Philippe Gambette, Vincent Berry and Christophe Paul. The structure of level-k phylogenetic networks. In CPM09, Vol. 5577:289-300 of LNCS, springer, 2009.
Keywords: coalescent, explicit network, galled tree, level k phylogenetic network, phylogenetic network, Program Recodon.
Note: http://hal-lirmm.ccsd.cnrs.fr/lirmm-00371485/en/.

Toggle abstract

@InProceedings{GBP2009,
AUTHOR = {Gambette, Philippe and Berry, Vincent and Paul, Christophe},
TITLE = {The structure of level-k phylogenetic networks},
YEAR = {2009},
BOOKTITLE = {CPM09},
VOLUME = {5577},
PAGES = {289-300},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-642-02441-2_26},
NOTE = {http://hal-lirmm.ccsd.cnrs.fr/lirmm-00371485/en/},
KEYWORDS = {coalescent, explicit network, galled tree, level k phylogenetic network, phylogenetic network, Program Recodon}
}

18

Daniel H. Huson, Regula Rupp, Vincent Berry, Philippe Gambette and Christophe Paul. Computing Galled Networks from Real Data. In ISMBECCB09, Vol. 25(12):i85-i93 of BIO, 2009.
Keywords: abstract network, cluster containment, explicit network, FPT, from clusters, from rooted trees, galled network, NP complete, phylogenetic network, phylogeny, polynomial, Program Dendroscope, reconstruction.
Note: http://hal-lirmm.ccsd.cnrs.fr/lirmm-00368545/en/.

Toggle abstract

@InProceedings{HRBGP2009,
AUTHOR = {Huson, Daniel H. and Rupp, Regula and Berry, Vincent and Gambette, Philippe and Paul, Christophe},
TITLE = {Computing Galled Networks from Real Data},
YEAR = {2009},
BOOKTITLE = {ISMBECCB09},
VOLUME = {25},
NUMBER = {12},
PAGES = {i85-i93},
SERIES = {BIO},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp217},
NOTE = {http://hal-lirmm.ccsd.cnrs.fr/lirmm-00368545/en/},
ANNOTE = {BIBUPDATE : 20090312},
KEYWORDS = {abstract network, cluster containment, explicit network, FPT, from clusters, from rooted trees, galled network, NP complete, phylogenetic network, phylogeny, polynomial, Program Dendroscope, reconstruction}
}

19

Lichen Bao and Sergey Bereg. Counting Faces in Split Networks. In ISBRA09, Vol. 5251:284-295 of LNCS, 2009.
Note: http://dx.doi.org/10.1007/978-3-642-01551-9_12.

Toggle abstract

@InProceedings{BaoBereg2009,
AUTHOR = {Bao, Lichen and Bereg, Sergey},
TITLE = {Counting Faces in Split Networks},
YEAR = {2009},
BOOKTITLE = {ISBRA09},
VOLUME = {5251},
PAGES = {284-295},
SERIES = {LNCS},
URL = {http://dx.doi.org/10.1007/978-3-642-01551-9_12},
NOTE = {http://dx.doi.org/10.1007/978-3-642-01551-9_12}
}

20

Martin Lott, Andreas Spillner, Katharina Huber and Vincent Moulton. PADRE: A Package for Analyzing and Displaying Reticulate Evolution. In BIO, Vol. 25(9):1199-1200, 2009.
Keywords: duplication, explicit network, from multilabeled tree, phylogenetic network, phylogeny, Program PADRE, reconstruction, software.
Note: http://dx.doi.org/10.1093/bioinformatics/btp133.

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@Article{LSHM2009,
AUTHOR = {Lott, Martin and Spillner, Andreas and Huber, Katharina and Moulton, Vincent},
TITLE = {PADRE: A Package for Analyzing and Displaying Reticulate Evolution},
YEAR = {2009},
JOURNAL = {BIO},
VOLUME = {25},
NUMBER = {9},
PAGES = {1199-1200},
URL = {http://dx.doi.org/10.1093/bioinformatics/btp133},
NOTE = {http://dx.doi.org/10.1093/bioinformatics/btp133},
KEYWORDS = {duplication, explicit network, from multilabeled tree, phylogenetic network, phylogeny, Program PADRE, reconstruction, software}
}

21

Peter J. Humphries and Charles Semple. Note on the hybridization number and subtree distance in phylogenetics. In Applied Mathematics Letters, Vol. 22(4):611-615, 2009.
Keywords: explicit network, minimum number, phylogenetic network, phylogeny, SPR distance.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/HS08.pdf.

@Article{HumphriesSemple2009,
AUTHOR = {Humphries, Peter J. and Semple, Charles},
TITLE = {Note on the hybridization number and subtree distance in phylogenetics},
YEAR = {2009},
JOURNAL = {Applied Mathematics Letters},
VOLUME = {22},
NUMBER = {4},
PAGES = {611-615},
URL = {http://dx.doi.org/10.1016/j.aml.2008.08.018},
NOTE = {http://www.math.canterbury.ac.nz/~c.semple/papers/HS08.pdf},
KEYWORDS = {explicit network, minimum number, phylogenetic network, phylogeny, SPR distance}
}

22

Laxmi Parida, Asif Javed, Marta Melé, Francesc Calafell, Jaume Bertranpetit and Genographic Consortium. Minimizing recombinations in consensus networks for phylogeographic studies. In BMCB, Vol. 10(Suppl 1):S72, 2009.
Note: Selected papers from the Seventh Asia-Pacific Bioinformatics Conference (APBC 2009), http://dx.doi.org/10.1186/1471-2105-10-S1-S72.

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@Article{PJMCBG2009,
AUTHOR = {Parida, Laxmi and Javed, Asif and Mel{\~A}�, Marta and Calafell, Francesc and Bertranpetit, Jaume and Consortium, Genographic},
TITLE = {Minimizing recombinations in consensus networks for phylogeographic studies},
YEAR = {2009},
JOURNAL = {BMCB},
VOLUME = {10},
NUMBER = {Suppl 1},
PAGES = {S72},
URL = {http://dx.doi.org/10.1186/1471-2105-10-S1-S72},
NOTE = {Selected papers from the Seventh Asia-Pacific Bioinformatics Conference (APBC 2009), http://dx.doi.org/10.1186/1471-2105-10-S1-S72}
}

23

Robert G. Beiko and Mark A. Ragan. Untangling Hybrid Phylogenetic Signals: Horizontal Gene Transfer and Artifacts of Phylogenetic Reconstruction. In Horizontal Gene Transfer, Vol. 532:241-256 of Methods in Molecular Biology, 2009.
Note: http://dx.doi.org/10.1007/978-1-60327-853-9_14.

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@InBook{BeikoRagan2009,
AUTHOR = {Beiko, Robert G. and Ragan, Mark A.},
TITLE = {Untangling Hybrid Phylogenetic Signals: Horizontal Gene Transfer and Artifacts of Phylogenetic Reconstruction},
YEAR = {2009},
BOOKTITLE = {Horizontal Gene Transfer},
VOLUME = {532},
PAGES = {241-256},
SERIES = {Methods in Molecular Biology},
URL = {http://dx.doi.org/10.1007/978-1-60327-853-9_14},
NOTE = {http://dx.doi.org/10.1007/978-1-60327-853-9_14}
}

24

Maria S. Poptsova. Testing Phylogenetic Methods to Identify Horizontal Gene Transfer. In Horizontal Gene Transfer, Pages 227-240, 2009.
Note: http://dx.doi.org/10.1007/978-1-60327-853-9_13.

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@InBook{Poptsova2009,
AUTHOR = {Poptsova, Maria S.},
TITLE = {Testing Phylogenetic Methods to Identify Horizontal Gene Transfer},
YEAR = {2009},
BOOKTITLE = {Horizontal Gene Transfer},
PAGES = {227-240},
SERIES = {Methods in Molecular Biology},
URL = {http://dx.doi.org/10.1007/978-1-60327-853-9_13},
NOTE = {http://dx.doi.org/10.1007/978-1-60327-853-9_13}
}

25

Francesc Rosselló and Gabriel Valiente. All that Glisters is not Galled. In MBIO, Vol. 221(1):54-59, 2009.
Keywords: galled tree, phylogenetic network, phylogeny.
Note: http://arxiv.org/abs/0904.2448.

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@Article{RosselloValiente2009,
AUTHOR = {Rossell{\~A}�, Francesc and Valiente, Gabriel},
TITLE = {All that Glisters is not Galled},
YEAR = {2009},
JOURNAL = {MBIO},
VOLUME = {221},
NUMBER = {1},
PAGES = {54-59},
URL = {http://dx.doi.org/10.1016/j.mbs.2009.06.007},
NOTE = {http://arxiv.org/abs/0904.2448},
KEYWORDS = {galled tree, phylogenetic network, phylogeny}
}

26

Sarah C. Ayling and Terence A. Brown. Novel methodology for construction and pruning of quasi-median networks. In BMCB, Vol. 9:115, 2009.
Keywords: abstract network, from sequences, median network, phylogenetic network, phylogeny, quasi-median network, reconstruction.
Note: http://dx.doi.org/10.1186/1471-2105-9-115.

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@Article{AylingBrown2009,
AUTHOR = {Ayling, Sarah C. and Brown, Terence A.},
TITLE = {Novel methodology for construction and pruning of quasi-median networks},
YEAR = {2009},
JOURNAL = {BMCB},
VOLUME = {9},
PAGES = {115},
URL = {http://dx.doi.org/10.1186/1471-2105-9-115},
NOTE = {http://dx.doi.org/10.1186/1471-2105-9-115},
KEYWORDS = {abstract network, from sequences, median network, phylogenetic network, phylogeny, quasi-median network, reconstruction}
}

27

Stefan Grünewald, Jacobus Koolen and Woo-Sun Lee. Quartets in maximal weakly compatible split systems. In Applied Mathematics Letters, Vol. 22(6):1604-1608, 2009.
Note: http://dx.doi.org/10.1016/j.aml.2009.05.006.

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@Article{GKL2009,
AUTHOR = {Gr{\~A}�newald, Stefan and Koolen, Jacobus and Lee, Woo-Sun},
TITLE = {Quartets in maximal weakly compatible split systems},
YEAR = {2009},
JOURNAL = {Applied Mathematics Letters},
VOLUME = {22},
NUMBER = {6},
PAGES = {1604-1608},
URL = {http://dx.doi.org/10.1016/j.aml.2009.05.006},
NOTE = {http://dx.doi.org/10.1016/j.aml.2009.05.006}
}

28

Martin Lott. New Methods for Constructing Phylogenetic Networks from Multi-Labelled Trees. PhD thesis, University of East Anglia, U.K., 2009.
Keywords: duplication, explicit network, from multilabeled tree, phylogenetic network, phylogeny, Program PADRE, reconstruction, software.
Note: http://www.ic0.net/thesis-martin-final.pdf.

@PhdThesis{Lott2009,
AUTHOR = {Lott, Martin},
TITLE = {New Methods for Constructing Phylogenetic Networks from Multi-Labelled Trees},
YEAR = {2009},
SCHOOL = {University of East Anglia, U.K.},
NOTE = {http://www.ic0.net/thesis-martin-final.pdf},
KEYWORDS = {duplication, explicit network, from multilabeled tree, phylogenetic network, phylogeny, Program PADRE, reconstruction, software}
}

29

Klaus Schliep. Some applications of statistical phylogenetics. PhD thesis, Massey University, New Zealand, 2009.
Keywords: abstract network, phylogenetic network, Program Phangorn, reconstruction, split network.
Note: http://muir.massey.ac.nz/handle/10179/931.

@PhdThesis{Schliep2009,
AUTHOR = {Schliep, Klaus},
TITLE = {Some applications of statistical phylogenetics},
YEAR = {2009},
SCHOOL = {Massey University, New Zealand},
NOTE = {http://muir.massey.ac.nz/handle/10179/931},
KEYWORDS = {abstract network, phylogenetic network, Program Phangorn, reconstruction, split network}
}

30

Leo van Iersel, Judith Keijsper, Steven Kelk, Leen Stougie, Ferry Hagen and Teun Boekhout. Constructing Level-2 Phylogenetic Networks from Triplets. In TCBB, Vol. 6(4):667-681, 2009.
Note: http://www.win.tue.nl/~liersel/level2full.pdf.

@Article{IKKSHB2009,
AUTHOR = {van Iersel, Leo and Keijsper, Judith and Kelk, Steven and Stougie, Leen and Hagen, Ferry and Boekhout, Teun},
TITLE = {Constructing Level-2 Phylogenetic Networks from Triplets},
YEAR = {2009},
JOURNAL = {TCBB},
VOLUME = {6},
NUMBER = {4},
PAGES = {667-681},
URL = {http://dx.doi.org/10.1109/TCBB.2009.22},
NOTE = {http://www.win.tue.nl/~liersel/level2full.pdf}
}

31

Josh Voorkamp né Collins. Rekernelisation Algorithms in Hybrid Phylogenies. Master's thesis, University of Canterbury, New Zealand, 2009.
Keywords: agreement forest, explicit network, FPT, from rooted trees, from unrooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, software.
Note: http://hdl.handle.net/10092/2852.

@MastersThesis{Collins2009,
AUTHOR = {Voorkamp n{\~A}� Collins, Josh},
TITLE = {Rekernelisation Algorithms in Hybrid Phylogenies},
YEAR = {2009},
SCHOOL = {University of Canterbury, New Zealand},
NOTE = {http://hdl.handle.net/10092/2852},
KEYWORDS = {agreement forest, explicit network, FPT, from rooted trees, from unrooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, software}
}

32

Mark A. Ragan. Trees and networks before and after Darwin. In Biology Direct, Vol. 4(43), 2009.
Keywords: abstract network, explicit network, phylogenetic network, phylogeny, survey, visualization.
Note: http://dx.doi.org/10.1186/1745-6150-4-43.

Toggle abstract

@Article{Ragan2009,
AUTHOR = {Ragan, Mark A.},
TITLE = {Trees and networks before and after Darwin},
YEAR = {2009},
JOURNAL = {Biology Direct},
VOLUME = {4},
NUMBER = {43},
URL = {http://dx.doi.org/10.1186/1745-6150-4-43},
NOTE = {http://dx.doi.org/10.1186/1745-6150-4-43},
KEYWORDS = {abstract network, explicit network, phylogenetic network, phylogeny, survey, visualization}
}

33

Ali Tofigh. Using Trees to Capture Reticulate Evolution, Lateral Gene Transfers and Cancer Progression. PhD thesis, KTH Royal Institute of Technology, Sweden, 2009.
Keywords: duplication, dynamic programming, from multilabeled tree, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: http://kth.diva-portal.org/smash/record.jsf?pid=diva2:220830&searchId=1.

@PhdThesis{Tofigh2009,
AUTHOR = {Tofigh, Ali},
TITLE = {Using Trees to Capture Reticulate Evolution, Lateral Gene Transfers and Cancer Progression},
YEAR = {2009},
SCHOOL = {KTH Royal Institute of Technology, Sweden},
NOTE = {http://kth.diva-portal.org/smash/record.jsf?pid=diva2:220830{\&}searchId=1},
KEYWORDS = {duplication, dynamic programming, from multilabeled tree, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction}
}

34

Ali Tofigh, Joel Sjöstrand, Bengt Sennblad, Lars Arvestad and Jens Lagergren. Detecting LGTs using a novel probabilistic model integrating duplications, LGTs, losses, rate variation, and sequence evolution. 2009.
Keywords: duplication, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction.
Note: http://kth.diva-portal.org/smash/record.jsf?searchId=1&pid=diva2:233574.

@Misc{TSSAL2009,
AUTHOR = {Tofigh, Ali and Sj{\~A}�strand, Joel and Sennblad, Bengt and Arvestad, Lars and Lagergren, Jens},
TITLE = {Detecting LGTs using a novel probabilistic model integrating duplications, LGTs, losses, rate variation, and sequence evolution},
YEAR = {2009},
NOTE = {http://kth.diva-portal.org/smash/record.jsf?searchId=1{\&}pid=diva2:233574},
KEYWORDS = {duplication, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction}
}

35

Leo van Iersel and Steven Kelk. A short note on the tractability of constructing phylogenetic networks from clusters. 2009.
Keywords: from clusters, from triplets, level k phylogenetic network, phylogenetic network, polynomial, reconstruction.
Note: http://arxiv.org/abs/0912.4502.

@Misc{IerselKelk2009,
AUTHOR = {van Iersel, Leo and Kelk, Steven},
TITLE = {A short note on the tractability of constructing phylogenetic networks from clusters},
YEAR = {2009},
NOTE = {http://arxiv.org/abs/0912.4502},
KEYWORDS = {from clusters, from triplets, level k phylogenetic network, phylogenetic network, polynomial, reconstruction}
}

36

Gabriel Valiente. Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R. Pages 184-208, Taylor & Francis/CRC Press, 2009.
Keywords: counting, distance between networks, galled tree, generation, phylogenetic network, phylogeny, survey, time consistent network, tree sibling network, tree-child network.
Note: http://books.google.fr/books?id=F4YIIUWb7yMC.

@InBook{Valiente2009,
AUTHOR = {Valiente, Gabriel},
TITLE = {Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R},
YEAR = {2009},
PAGES = {184-208},
PUBLISHER = {Taylor {\&} Francis/CRC Press},
URL = {http://dx.doi.org/10.1201/9781420069747},
NOTE = {http://books.google.fr/books?id=F4YIIUWb7yMC},
KEYWORDS = {counting, distance between networks, galled tree, generation, phylogenetic network, phylogeny, survey, time consistent network, tree sibling network, tree-child network}
}

37

Martin Lott, Andreas Spillner, Katharina Huber, Anna Petri, Bengt Oxelman and Vincent Moulton. Inferring polyploid phylogenies from multiply-labeled gene trees. In BMCEB, Vol. 9:216, 2009.
Keywords: duplication, explicit network, from multilabeled tree, phylogenetic network, phylogeny, Program PADRE, reconstruction.
Note: http://dx.doi.org/10.1186/1471-2148-9-216.

Toggle abstract

@Article{LSHPOM2009,
AUTHOR = {Lott, Martin and Spillner, Andreas and Huber, Katharina and Petri, Anna and Oxelman, Bengt and Moulton, Vincent},
TITLE = {Inferring polyploid phylogenies from multiply-labeled gene trees},
YEAR = {2009},
JOURNAL = {BMCEB},
VOLUME = {9},
PAGES = {216},
URL = {http://dx.doi.org/10.1186/1471-2148-9-216},
NOTE = {http://dx.doi.org/10.1186/1471-2148-9-216},
KEYWORDS = {duplication, explicit network, from multilabeled tree, phylogenetic network, phylogeny, Program PADRE, reconstruction}
}

38

Laura S. Kubatko. Identifying Hybridization Events in the Presence of Coalescence via Model Selection. In Systematic Biology, Vol. 58(5):478-488, 2009.
Keywords: AIC, BIC, branch length, coalescent, explicit network, from rooted trees, from species tree, hybridization, lineage sorting, model selection, phylogenetic network, phylogeny, statistical model.
Note: http://dx.doi.org/10.1093/sysbio/syp055.

@Article{Kubatko2009,
AUTHOR = {Kubatko, Laura S.},
TITLE = {Identifying Hybridization Events in the Presence of Coalescence via Model Selection},
YEAR = {2009},
JOURNAL = {Systematic Biology},
VOLUME = {58},
NUMBER = {5},
PAGES = {478-488},
URL = {http://dx.doi.org/10.1093/sysbio/syp055},
NOTE = {http://dx.doi.org/10.1093/sysbio/syp055},
KEYWORDS = {AIC, BIC, branch length, coalescent, explicit network, from rooted trees, from species tree, hybridization, lineage sorting, model selection, phylogenetic network, phylogeny, statistical model}
}

39

Chen Meng and Laura S. Kubatko. Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model. In Theoretical Population Biology, Vol. 75(1):35-45, 2009.
Keywords: bayesian, coalescent, from network, from rooted trees, hybridization, likelihood, lineage sorting, phylogenetic network, phylogeny, statistical model.
Note: http://dx.doi.org/10.1016/j.tpb.2008.10.004.

Toggle abstract

@Article{MengKubatko2009,
AUTHOR = {Meng, Chen and Kubatko, Laura S.},
TITLE = {Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model},
YEAR = {2009},
JOURNAL = {Theoretical Population Biology},
VOLUME = {75},
NUMBER = {1},
PAGES = {35-45},
URL = {http://dx.doi.org/10.1016/j.tpb.2008.10.004},
NOTE = {http://dx.doi.org/10.1016/j.tpb.2008.10.004},
KEYWORDS = {bayesian, coalescent, from network, from rooted trees, hybridization, likelihood, lineage sorting, phylogenetic network, phylogeny, statistical model}
}

40

Marc Thuillard and Didier Fraix-Burnet. Phylogenetic Applications of the Minimum Contradiction Approach on Continuous Characters. In Evolutionary Bioinformatics, Vol. 5:53-46, 2009.
Keywords: from continuous characters, minimum contradiction, phylogenetic network, phylogeny, split, split network.
Note: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2747132/.

@Article{ThuillardFraixbrunet2009,
AUTHOR = {Thuillard, Marc and Fraix-Burnet, Didier},
TITLE = {Phylogenetic Applications of the Minimum Contradiction Approach on Continuous Characters},
YEAR = {2009},
JOURNAL = {Evolutionary Bioinformatics},
VOLUME = {5},
PAGES = {53-46},
URL = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2747132/},
NOTE = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2747132/},
KEYWORDS = {from continuous characters, minimum contradiction, phylogenetic network, phylogeny, split, split network}
}

41

Bui Quang Minh, Steffen Klaere and Arndt von Haeseler. Taxon Selection under Split Diversity. In Systematic Biology, Vol. 58(6):586-594, 2009.
Keywords: abstract network, circular split system, diversity, from network, phylogenetic network, split network.
Note: http://dx.doi.org/10.1093/sysbio/syp058.

Toggle abstract

@Article{MKH2009,
AUTHOR = {Minh, Bui Quang and Klaere, Steffen and von Haeseler, Arndt},
TITLE = {Taxon Selection under Split Diversity},
YEAR = {2009},
JOURNAL = {Systematic Biology},
VOLUME = {58},
NUMBER = {6},
PAGES = {586-594},
URL = {http://dx.doi.org/10.1093/sysbio/syp058},
NOTE = {http://dx.doi.org/10.1093/sysbio/syp058},
KEYWORDS = {abstract network, circular split system, diversity, from network, phylogenetic network, split network}
}

42

Bui Quang Minh, Fabio Pardi, Steffen Klaere and Arndt von Haeseler. Budgeted Phylogenetic Diversity on Circular Split Systems. In TCBB, Vol. 6(1):22-29, 2009.
Keywords: abstract network, circular split system, dynamic programming, from network, phylogenetic network, polynomial, split, split network.
Note: http://dx.doi.org/10.1109/TCBB.2008.54.

Toggle abstract

@Article{MPKH2009,
AUTHOR = {Minh, Bui Quang and Pardi, Fabio and Klaere, Steffen and von Haeseler, Arndt},
TITLE = {Budgeted Phylogenetic Diversity on Circular Split Systems},
YEAR = {2009},
JOURNAL = {TCBB},
VOLUME = {6},
NUMBER = {1},
PAGES = {22-29},
URL = {http://dx.doi.org/10.1109/TCBB.2008.54},
NOTE = {http://dx.doi.org/10.1109/TCBB.2008.54},
KEYWORDS = {abstract network, circular split system, dynamic programming, from network, phylogenetic network, polynomial, split, split network}
}

43

Qiong Wu. Phylogenetic Networks: New Constructions and Applications. PhD thesis, Université of East Anglia, U.K., 2009.
Keywords: abstract network, phylogenetic network, phylogeny, reconstruction, split network.
Note: http://ethos.bl.uk/OrderDetails.do?did=1&uin=uk.bl.ethos.514315.

@PhdThesis{Wu2009,
AUTHOR = {Wu, Qiong},
TITLE = {Phylogenetic Networks: New Constructions and Applications},
YEAR = {2009},
SCHOOL = {Universit{\~A}� of East Anglia, U.K.},
NOTE = {http://ethos.bl.uk/OrderDetails.do?did=1{\&}uin=uk.bl.ethos.514315},
KEYWORDS = {abstract network, phylogenetic network, phylogeny, reconstruction, split network}
}

44

Poornima Venugopal. Improving layout of phylogenetic network produced by PADRE. Master's thesis, University of Texas at Dallas, U.S.A., 2009.
Keywords: explicit network, phylogenetic network, Program PADRE, visualization.
Note: http://proquest.umi.com/pqdlink?did=2026498501&sid=1&Fmt=2&clientId=176295&RQT=309&VName=PQD.

@MastersThesis{Venugopal2009,
AUTHOR = {Venugopal, Poornima},
TITLE = {Improving layout of phylogenetic network produced by PADRE},
YEAR = {2009},
SCHOOL = {University of Texas at Dallas, U.S.A.},
NOTE = {http://proquest.umi.com/pqdlink?did=2026498501{\&}sid=1{\&}Fmt=2{\&}clientId=176295{\&}RQT=309{\&}VName=PQD},
KEYWORDS = {explicit network, phylogenetic network, Program PADRE, visualization}
}

45

Lichen Bao. Phylogenetic network construction and the application. PhD thesis, University of Texas at Dallas, U.S.A., 2009.
Keywords: from distances, phylogenetic network, phylogeny, reconstruction, split, split network.
Note: http://proquest.umi.com/pqdlink?did=1952801881&sid=1&Fmt=6&clientId=176295&RQT=309&VName=PQD.

@PhdThesis{Bao2009,
AUTHOR = {Bao, Lichen},
TITLE = {Phylogenetic network construction and the application},
YEAR = {2009},
SCHOOL = {University of Texas at Dallas, U.S.A.},
NOTE = {http://proquest.umi.com/pqdlink?did=1952801881{\&}sid=1{\&}Fmt=6{\&}clientId=176295{\&}RQT=309{\&}VName=PQD},
KEYWORDS = {from distances, phylogenetic network, phylogeny, reconstruction, split, split network}
}

46

Simon Joly, Patricia A. McLenachan and Peter J. Lockhart. A Statistical Approach for Distinguishing Hybridization and Incomplete Lineage Sorting. In The American Naturalist, Vol. 174(2):E54-E70, 2009.
Keywords: hybridization, lineage sorting, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: http://www.plantevolution.org/pdf/Joly&al_2009_AmNat.pdf.

Toggle abstract

@Article{JML2009,
AUTHOR = {Joly, Simon and McLenachan, Patricia A. and Lockhart, Peter J.},
TITLE = {A Statistical Approach for Distinguishing Hybridization and Incomplete Lineage Sorting},
YEAR = {2009},
JOURNAL = {The American Naturalist},
VOLUME = {174},
NUMBER = {2},
PAGES = {E54-E70},
URL = {http://dx.doi.org/10.1086/600082},
NOTE = {http://www.plantevolution.org/pdf/Joly{\&}al_2009_AmNat.pdf},
KEYWORDS = {hybridization, lineage sorting, phylogenetic network, phylogeny, reconstruction, statistical model}
}

47

Poornima Venugopal and Sergey Bereg. Layout of Phylogenetic Networks and Multi-Labeled Trees. In BIOT'09, Pages 91, 2009.
Keywords: explicit network, phylogenetic network, phylogeny, Program PADRE, visualization.
Note: http://www.biotconf.org/PDFs/1456.pdf.

@InProceedings{VenugopalBereg2009,
AUTHOR = {Venugopal, Poornima and Bereg, Sergey},
TITLE = {Layout of Phylogenetic Networks and Multi-Labeled Trees},
YEAR = {2009},
BOOKTITLE = {BIOT'09},
PAGES = {91},
NOTE = {http://www.biotconf.org/PDFs/1456.pdf},
KEYWORDS = {explicit network, phylogenetic network, phylogeny, Program PADRE, visualization}
}

48

Chris Whidden. A Unifying View on Approximation and FPT of Agreement Forests. Master's thesis, Dalhousie University, Canada, 2009.
Keywords: agreement forest, approximation, explicit network, FPT, from rooted trees, hybridization, phylogenetic network, phylogeny, reconstruction, SPR distance.
Note: http://web.cs.dal.ca/~whidden/MCSThesis09.pdf.

@MastersThesis{Whidden2009,
AUTHOR = {Whidden, Chris},
TITLE = {A Unifying View on Approximation and FPT of Agreement Forests},
YEAR = {2009},
SCHOOL = {Dalhousie University, Canada},
URL = {http://dx.doi.org/10.1007/978-3-642-04241-6_32},
NOTE = {http://web.cs.dal.ca/~whidden/MCSThesis09.pdf},
KEYWORDS = {agreement forest, approximation, explicit network, FPT, from rooted trees, hybridization, phylogenetic network, phylogeny, reconstruction, SPR distance}
}

49

Vincent Moulton and Katharina Huber. Split Networks. A tool for exploring complex evolutionary relationships in molecular data. In Philippe Lemey, Marco Salemi and Anne-Mieke Vandamme editors, The Phylogenetic Handbook, Cambridge University Press, 2009.
Keywords: abstract network, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network.

@InBook{MoultonHuber2009,
AUTHOR = {Moulton, Vincent and Huber, Katharina},
TITLE = {Split Networks. A tool for exploring complex evolutionary relationships in molecular data},
YEAR = {2009},
BOOKTITLE = {The Phylogenetic Handbook},
EDITOR = {Lemey, Philippe and Salemi, Marco and Vandamme, Anne-Mieke},
PUBLISHER = {Cambridge University Press},
URL = {http://dx.doi.org/10.1017/cbo9780511819049.023},
KEYWORDS = {abstract network, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network}
}

50

Chris Whidden and Norbert Zeh. A Unifying View on Approximation and FPT of Agreement Forests. In WABI09, Vol. 5724:390-402 of LNCS, Springer, 2009.
Keywords: agreement forest, approximation, explicit network, FPT, minimum number, phylogenetic network, phylogeny, reconstruction.
Note: https://www.cs.dal.ca/sites/default/files/technical_reports/CS-2009-02.pdf.

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@InProceedings{WhiddenZeh2009,
AUTHOR = {Whidden, Chris and Zeh, Norbert},
TITLE = {A Unifying View on Approximation and FPT of Agreement Forests},
YEAR = {2009},
BOOKTITLE = {WABI09},
VOLUME = {5724},
PAGES = {390-402},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {http://dx.doi.org/10.1007/978-3-642-04241-6_32},
NOTE = {https://www.cs.dal.ca/sites/default/files/technical_reports/CS-2009-02.pdf},
KEYWORDS = {agreement forest, approximation, explicit network, FPT, minimum number, phylogenetic network, phylogeny, reconstruction}
}

2008

1

Gabriel Cardona, Francesc Rosselló and Gabriel Valiente. Tripartitions do not always discriminate phylogenetic networks. In MBIO, Vol. 211(2):356-370, 2008.
Keywords: distance between networks, phylogenetic network, phylogeny, Program Bio PhyloNetwork, tree-child network, tripartition distance.
Note: http://arxiv.org/abs/0707.2376, slides available at http://www.newton.cam.ac.uk/webseminars/pg+ws/2007/plg/plgw01/0904/valiente/.

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@Article{CRV2008,
AUTHOR = {Cardona, Gabriel and Rossell{\~A}�, Francesc and Valiente, Gabriel},
TITLE = {Tripartitions do not always discriminate phylogenetic networks.},
YEAR = {2008},
JOURNAL = {MBIO},
VOLUME = {211},
NUMBER = {2},
PAGES = {356-370},
URL = {http://dx.doi.org/10.1016/j.mbs.2007.11.003},
NOTE = {http://arxiv.org/abs/0707.2376, slides available at http://www.newton.cam.ac.uk/webseminars/pg+ws/2007/plg/plgw01/0904/valiente/},
ANNOTE = {BIBUPDATE : 20080516},
KEYWORDS = {distance between networks, phylogenetic network, phylogeny, Program Bio PhyloNetwork, tree-child network, tripartition distance}
}

2

Philippe Gambette and Daniel H. Huson. Improved Layout of Phylogenetic Networks. In TCBB, Vol. 5(3):472-479, 2008.
Keywords: abstract network, heuristic, phylogenetic network, phylogeny, Program SplitsTree, software, split network, visualization.
Note: http://hal-lirmm.ccsd.cnrs.fr/lirmm-00309694/en/.

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@Article{GambetteHuson2008,
AUTHOR = {Gambette, Philippe and Huson, Daniel H.},
TITLE = {Improved Layout of Phylogenetic Networks},
YEAR = {2008},
JOURNAL = {TCBB},
VOLUME = {5},
NUMBER = {3},
PAGES = {472-479},
URL = {http://dx.doi.org/10.1109/TCBB.2007.1046},
NOTE = {http://hal-lirmm.ccsd.cnrs.fr/lirmm-00309694/en/},
ANNOTE = {BIBUPDATE : 20080301},
KEYWORDS = {abstract network, heuristic, phylogenetic network, phylogeny, Program SplitsTree, software, split network, visualization}
}

3

Stefan Grünewald, Katharina Huber and Qiong Wu. Two novel closure rules for constructing phylogenetic super-networks. In BMB, Vol. 70(7):1906-1924, 2008.
Keywords: abstract network, from splits, from unrooted trees, phylogenetic network, phylogeny, Program MY CLOSURE, reconstruction, supernetwork.
Note: http://arxiv.org/abs/0709.0283, slides available at http://www.newton.cam.ac.uk/webseminars/pg+ws/2007/plg/plgw01/0904/huber/.

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@Article{GHW2008,
AUTHOR = {Gr{\~A}�newald, Stefan and Huber, Katharina and Wu, Qiong},
TITLE = {Two novel closure rules for constructing phylogenetic super-networks},
YEAR = {2008},
JOURNAL = {BMB},
VOLUME = {70},
NUMBER = {7},
PAGES = {1906-1924},
URL = {http://dx.doi.org/10.1007/s11538-008-9331-4},
NOTE = {http://arxiv.org/abs/0709.0283, slides available at http://www.newton.cam.ac.uk/webseminars/pg+ws/2007/plg/plgw01/0904/huber/},
ANNOTE = {BIBUPDATE : 20071002},
KEYWORDS = {abstract network, from splits, from unrooted trees, phylogenetic network, phylogeny, Program MY CLOSURE, reconstruction, supernetwork}
}

4

Leo van Iersel, Judith Keijsper, Steven Kelk, Leen Stougie, Ferry Hagen and Teun Boekhout. Constructing level-2 phylogenetic networks from triplets. In RECOMB08, Vol. 4955:450-462 of LNCS, springer, 2008.
Keywords: explicit network, from triplets, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, polynomial, Program Level2, reconstruction.
Note: http://homepages.cwi.nl/~iersel/level2full.pdf. An appendix with proofs can be found here http://arxiv.org/abs/0707.2890.

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@InProceedings{IKKSHB2008,
AUTHOR = {van Iersel, Leo and Keijsper, Judith and Kelk, Steven and Stougie, Leen and Hagen, Ferry and Boekhout, Teun},
TITLE = {Constructing level-2 phylogenetic networks from triplets},
YEAR = {2008},
BOOKTITLE = {RECOMB08},
VOLUME = {4955},
PAGES = {450-462},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1109/TCBB.2009.22},
NOTE = {http://homepages.cwi.nl/~iersel/level2full.pdf. An appendix with proofs can be found here http://arxiv.org/abs/0707.2890},
ANNOTE = {BIBUPDATE : 20080124},
KEYWORDS = {explicit network, from triplets, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, polynomial, Program Level2, reconstruction}
}

5

Iyad A. Kanj, Luay Nakhleh and Ge Xia. The Compatibility of Binary Characters on Phylogenetic Networks: Complexity and Parameterized Algorithms. In ALG, Vol. 51(2):99-128, 2008.
Keywords: perfect, phylogenetic network, phylogeny.
Note: http://www.cs.rice.edu/~nakhleh/Papers/algorithmica.pdf.

@Article{KNX2008,
AUTHOR = {Kanj, Iyad A. and Nakhleh, Luay and Xia, Ge},
TITLE = {The Compatibility of Binary Characters on Phylogenetic Networks: Complexity and Parameterized Algorithms},
YEAR = {2008},
JOURNAL = {ALG},
VOLUME = {51},
NUMBER = {2},
PAGES = {99-128},
URL = {http://dx.doi.org/10.1007/s00453-007-9046-1},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/algorithmica.pdf},
ANNOTE = {CITE : },
KEYWORDS = {perfect, phylogenetic network, phylogeny}
}

6

Andreas Spillner, Binh T. Nguyen and Vincent Moulton. Computing phylogenetic diversity for split systems. In TCBB, Vol. 5(2):235-244, 2008.
Keywords: abstract network, diversity, phylogenetic network, phylogeny, split.
Note: http://dx.doi.org/10.1109/TCBB.2007.70260, slides available at http://www.newton.cam.ac.uk/webseminars/pg+ws/2007/plg/plgw01/0906/spillner/.

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@Article{SNM2008,
AUTHOR = {Spillner, Andreas and Nguyen, Binh T. and Moulton, Vincent},
TITLE = {Computing phylogenetic diversity for split systems},
YEAR = {2008},
JOURNAL = {TCBB},
VOLUME = {5},
NUMBER = {2},
PAGES = {235-244},
URL = {http://dx.doi.org/10.1109/TCBB.2007.70260},
NOTE = {http://dx.doi.org/10.1109/TCBB.2007.70260, slides available at http://www.newton.cam.ac.uk/webseminars/pg+ws/2007/plg/plgw01/0906/spillner/},
ANNOTE = {BIBUPDATE : 20070924},
KEYWORDS = {abstract network, diversity, phylogenetic network, phylogeny, split}
}

7

Gabriel Cardona, Francesc Rosselló and Gabriel Valiente. A Perl Package and an Alignment Tool for Phylogenetic Networks. In BMCB, Vol. 9:175, 2008.
Keywords: distance between networks, phylogenetic network, phylogeny, Program Bio PhyloNetwork, tree sibling network, tree-child network.
Note: http://dx.doi.org/10.1186/1471-2105-9-175.

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@Article{CRV2008b,
AUTHOR = {Cardona, Gabriel and Rossell{\~A}�, Francesc and Valiente, Gabriel},
TITLE = {A Perl Package and an Alignment Tool for Phylogenetic Networks},
YEAR = {2008},
JOURNAL = {BMCB},
VOLUME = {9},
PAGES = {175},
URL = {http://dx.doi.org/10.1186/1471-2105-9-175},
NOTE = {http://dx.doi.org/10.1186/1471-2105-9-175},
ANNOTE = {BIBUPDATE : 20080506},
KEYWORDS = {distance between networks, phylogenetic network, phylogeny, Program Bio PhyloNetwork, tree sibling network, tree-child network}
}

8

Stephen J. Willson. Reconstruction of certain phylogenetic networks from the genomes at their leaves. In JTB, Vol. 252(2):185-376, 2008.
Keywords: labeling, polynomial.
Note: http://www.public.iastate.edu/~swillson/ReconstructNormalHomopap6.pdf.

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@Article{Willson2008,
AUTHOR = {Willson, Stephen J.},
TITLE = {Reconstruction of certain phylogenetic networks from the genomes at their leaves},
YEAR = {2008},
JOURNAL = {JTB},
VOLUME = {252},
NUMBER = {2},
PAGES = {185-376},
URL = {http://dx.doi.org/10.1016/j.jtbi.2008.02.015},
NOTE = {http://www.public.iastate.edu/~swillson/ReconstructNormalHomopap6.pdf},
ANNOTE = {BIBUPDATE : 20071216},
KEYWORDS = {labeling, polynomial}
}

9

Rune Lyngsø, Yun S. Song and Jotun Hein. Accurate Computation of Likelihoods in the Coalescent with Recombination via Parsimony. In RECOMB08, Vol. 4955:463-477 of LNCS, springer, 2008.
Keywords: coalescent, likelihood, phylogenetic network, phylogeny, recombination, statistical model.
Note: http://dx.doi.org/10.1007/978-3-540-78839-3_41.

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@InProceedings{LSH2008,
AUTHOR = {Lyngs{\~A}�, Rune and Song, Yun S. and Hein, Jotun},
TITLE = {Accurate Computation of Likelihoods in the Coalescent with Recombination via Parsimony},
YEAR = {2008},
BOOKTITLE = {RECOMB08},
VOLUME = {4955},
PAGES = {463-477},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-540-78839-3_41},
NOTE = {http://dx.doi.org/10.1007/978-3-540-78839-3_41},
ANNOTE = {BIBUPDATE : 20080506},
KEYWORDS = {coalescent, likelihood, phylogenetic network, phylogeny, recombination, statistical model}
}

10

Andreas W. M. Dress, Katharina Huber, Jacobus Koolen and Vincent Moulton. Compatible decompositions and block realizations of finite metrics. In EJC, Vol. 29(7):1617-1633, 2008.
Keywords: abstract network, block realization, from distances, phylogenetic network, phylogeny, realization, reconstruction.
Note: http://www.ims.nus.edu.sg/preprints/2007-21.pdf.

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@Article{DHKM2008,
AUTHOR = {Dress, Andreas W. M. and Huber, Katharina and Koolen, Jacobus and Moulton, Vincent},
TITLE = {Compatible decompositions and block realizations of finite metrics},
YEAR = {2008},
JOURNAL = {EJC},
VOLUME = {29},
NUMBER = {7},
PAGES = {1617-1633},
URL = {http://dx.doi.org/10.1016/j.ejc.2007.10.003},
NOTE = {http://www.ims.nus.edu.sg/preprints/2007-21.pdf},
ANNOTE = {BIBUPDATE : 20080303},
KEYWORDS = {abstract network, block realization, from distances, phylogenetic network, phylogeny, realization, reconstruction}
}

11

Tobias Kloepper and Daniel H. Huson. Drawing explicit phylogenetic networks and their integration into SplitsTree. In BMCEB, Vol. 8(22), 2008.
Keywords: explicit network, phylogenetic network, phylogeny, Program SplitsTree, software, split network, visualization.
Note: http://dx.doi.org/10.1186/1471-2148-8-22.

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@Article{KloepperHuson2008,
AUTHOR = {Kloepper, Tobias and Huson, Daniel H.},
TITLE = {Drawing explicit phylogenetic networks and their integration into SplitsTree},
YEAR = {2008},
JOURNAL = {BMCEB},
VOLUME = {8},
NUMBER = {22},
URL = {http://dx.doi.org/10.1186/1471-2148-8-22},
NOTE = {http://dx.doi.org/10.1186/1471-2148-8-22},
ANNOTE = {BIBUPDATE : 20080303},
KEYWORDS = {explicit network, phylogenetic network, phylogeny, Program SplitsTree, software, split network, visualization}
}

12

Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi and Giancarlo Mauri. The Comparison of Phylogenetic Networks: Algorithms and Complexity. In Ion Mandoiu and Alexander Zelikovsky editors, Bioinformatics Algorithms, John Wiley and Sons Ltd, 2008.
Keywords: phylogenetic network, phylogeny.
Note: http://www.amazon.com/gp/reader/0470097736/.

@InBook{BDDM2008,
AUTHOR = {Bonizzoni, Paola and Della Vedova, Gianluca and Dondi, Riccardo and Mauri, Giancarlo},
TITLE = {The Comparison of Phylogenetic Networks: Algorithms and Complexity},
YEAR = {2008},
BOOKTITLE = {Bioinformatics Algorithms},
EDITOR = {Mandoiu, Ion and Zelikovsky, Alexander},
PUBLISHER = {John Wiley and Sons Ltd},
NOTE = {http://www.amazon.com/gp/reader/0470097736/},
KEYWORDS = {phylogenetic network, phylogeny}
}

13

Steven M. Woolley, David Posada and Keith A. Crandall. A Comparison of Phylogenetic Network Methods Using Computer Simulation. In PLoS ONE, Vol. 3(4):e1913, 2008.
Keywords: abstract network, distance between networks, evaluation, median network, MedianJoining, minimum spanning network, NeighborNet, parsimony, phylogenetic network, phylogeny, Program Arlequin, Program CombineTrees, Program Network, Program SHRUB, Program SplitsTree, Program TCS, split decomposition.
Note: http://dx.doi.org/10.1371/journal.pone.0001913.

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@Article{WPC2008,
AUTHOR = {Woolley, Steven M. and Posada, David and Crandall, Keith A.},
TITLE = {A Comparison of Phylogenetic Network Methods Using Computer Simulation},
YEAR = {2008},
JOURNAL = {PLoS ONE},
VOLUME = {3},
NUMBER = {4},
PAGES = {e1913},
URL = {http://dx.doi.org/10.1371/journal.pone.0001913},
NOTE = {http://dx.doi.org/10.1371/journal.pone.0001913},
ANNOTE = {BIBUPDATE : 20080421},
KEYWORDS = {abstract network, distance between networks, evaluation, median network, MedianJoining, minimum spanning network, NeighborNet, parsimony, phylogenetic network, phylogeny, Program Arlequin, Program CombineTrees, Program Network, Program SHRUB, Program SplitsTree, Program TCS, split decomposition}
}

14

Gabriel Cardona, Mercè Llabrés, Francesc Rosselló and Gabriel Valiente. A Distance Metric for a Class of Tree-Sibling Phylogenetic Networks. In BIO, Vol. 24(13):1481-1488, 2008.
Keywords: distance between networks, phylogenetic network, phylogeny, polynomial, tree sibling network.
Note: http://dx.doi.org/10.1093/bioinformatics/btn231.

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@Article{CLRV2008b,
AUTHOR = {Cardona, Gabriel and Llabr{\~A}�s, Merc{\~A}� and Rossell{\~A}�, Francesc and Valiente, Gabriel},
TITLE = {A Distance Metric for a Class of Tree-Sibling Phylogenetic Networks},
YEAR = {2008},
JOURNAL = {BIO},
VOLUME = {24},
NUMBER = {13},
PAGES = {1481-1488},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn231},
NOTE = {http://dx.doi.org/10.1093/bioinformatics/btn231},
ANNOTE = {BIBUPDATE : 20080505, 20080520},
KEYWORDS = {distance between networks, phylogenetic network, phylogeny, polynomial, tree sibling network}
}

15

James B. Whitfield, Sydney A. Cameron, Daniel H. Huson and Mike Steel. Filtered Z-Closure Supernetworks for Extracting and Visualizing Recurrent Signal from Incongruent Gene Trees. In Systematic Biology, Vol. 57(6):939-947, 2008.
Keywords: abstract network, from unrooted trees, phylogenetic network, phylogeny, Program SplitsTree, split, split network, supernetwork.
Note: http://www.life.uiuc.edu/scameron/pdfs/Filtered%20Z-closure%20SystBiol.pdf.

@Article{WCHS2008,
AUTHOR = {Whitfield, James B. and Cameron, Sydney A. and Huson, Daniel H. and Steel, Mike},
TITLE = {Filtered Z-Closure Supernetworks for Extracting and Visualizing Recurrent Signal from Incongruent Gene Trees},
YEAR = {2008},
JOURNAL = {Systematic Biology},
VOLUME = {57},
NUMBER = {6},
PAGES = {939-947},
URL = {http://dx.doi.org/10.1080/10635150802552849},
NOTE = {http://www.life.uiuc.edu/scameron/pdfs/Filtered%20Z-closure%20SystBiol.pdf},
ANNOTE = {CITE : },
KEYWORDS = {abstract network, from unrooted trees, phylogenetic network, phylogeny, Program SplitsTree, split, split network, supernetwork}
}

16

Simone Linz. Reticulation in evolution. PhD thesis, Heinrich-Heine-University, Düsseldorf, Germany, 2008.
Keywords: agreement forest, FPT, from rooted trees, lateral gene transfer, phylogenetic network, phylogeny, SPR distance, statistical model.
Note: http://docserv.uni-duesseldorf.de/servlets/DocumentServlet?id=8505.

@PhdThesis{Linz2008,
AUTHOR = {Linz, Simone},
TITLE = {Reticulation in evolution},
YEAR = {2008},
SCHOOL = {Heinrich-Heine-University, D{\~A}�sseldorf, Germany},
NOTE = {http://docserv.uni-duesseldorf.de/servlets/DocumentServlet?id=8505},
ANNOTE = {CITE : },
KEYWORDS = {agreement forest, FPT, from rooted trees, lateral gene transfer, phylogenetic network, phylogeny, SPR distance, statistical model}
}

17

Leo van Iersel and Steven Kelk. Constructing the Simplest Possible Phylogenetic Network from Triplets. In ISAAC08, Vol. 5369:472-483 of LNCS, springer, 2008.
Keywords: explicit network, from triplets, galled tree, level k phylogenetic network, minimum number, phylogenetic network, phylogeny, polynomial, Program Marlon, Program Simplistic.
Note: http://arxiv.org/abs/0805.1859.

@InProceedings{IerselKelk2008,
AUTHOR = {van Iersel, Leo and Kelk, Steven},
TITLE = {Constructing the Simplest Possible Phylogenetic Network from Triplets},
YEAR = {2008},
BOOKTITLE = {ISAAC08},
VOLUME = {5369},
PAGES = {472-483},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-540-92182-0_43},
NOTE = {http://arxiv.org/abs/0805.1859},
ANNOTE = {CITE : },
KEYWORDS = {explicit network, from triplets, galled tree, level k phylogenetic network, minimum number, phylogenetic network, phylogeny, polynomial, Program Marlon, Program Simplistic}
}

18

Jesper Jansson and Wing-Kin Sung. The Maximum Agreement of Two Nested Phylogenetic Networks. In Oleg N. Terikhovsky and William N. Burton editors, New Topics in Theoretical Computer Science, Pages 119-141, Nova Publishers, 2008.
Keywords: dynamic programming, MASN, nested network, phylogenetic network, phylogeny, polynomial.
Note: http://www.df.lth.se/~jj/Publications/nested12_NTTCS2008_corrected.pdf.

@InBook{JanssonSung2008,
AUTHOR = {Jansson, Jesper and Sung, Wing-Kin},
TITLE = {The Maximum Agreement of Two Nested Phylogenetic Networks},
YEAR = {2008},
BOOKTITLE = {New Topics in Theoretical Computer Science},
PAGES = {119-141},
EDITOR = {Terikhovsky, Oleg N. and Burton, William N.},
PUBLISHER = {Nova Publishers},
NOTE = {http://www.df.lth.se/~jj/Publications/nested12_NTTCS2008_corrected.pdf},
ANNOTE = {BIBUPDATE : 20080520},
KEYWORDS = {dynamic programming, MASN, nested network, phylogenetic network, phylogeny, polynomial}
}

19

Cuong Than and Luay Nakhleh. SPR-based Tree Reconciliation: Non-binary Trees and Multiple Solutions. In APBC08, Pages 251-260, 2008.
Keywords: evaluation, from rooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program LatTrans, Program PhyloNet, reconstruction, SPR distance.
Note: http://www.cs.rice.edu/~nakhleh/Papers/apbc08.pdf.

@InProceedings{ThanNakhleh2008,
AUTHOR = {Than, Cuong and Nakhleh, Luay},
TITLE = {SPR-based Tree Reconciliation: Non-binary Trees and Multiple Solutions},
YEAR = {2008},
BOOKTITLE = {APBC08},
PAGES = {251-260},
URL = {http://dx.doi.org/10.1142/9781848161092_0027},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/apbc08.pdf},
ANNOTE = {BIBUPDATE : },
KEYWORDS = {evaluation, from rooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program LatTrans, Program PhyloNet, reconstruction, SPR distance}
}

20

Tobias Kloepper. Algorithms for the Calculation and Visualisation of Phylogenetic Networks. PhD thesis, Eberhard-Karls-Universität Tübingen, Germany, 2008.
Keywords: from rooted trees, from sequences, from unrooted trees, galled network, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network, visualization.
Note: https://publikationen.uni-tuebingen.de/xmlui/handle/10900/49159.

@PhdThesis{Kloepper2008,
AUTHOR = {Kloepper, Tobias},
TITLE = {Algorithms for the Calculation and Visualisation of Phylogenetic Networks},
YEAR = {2008},
SCHOOL = {Eberhard-Karls-Universit{\~A}�t T{\~A}�bingen, Germany},
NOTE = {https://publikationen.uni-tuebingen.de/xmlui/handle/10900/49159},
ANNOTE = {BIBUPDATE : 20080605},
KEYWORDS = {from rooted trees, from sequences, from unrooted trees, galled network, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network, visualization}
}

21

Daniel H. Huson and Regula Rupp. Summarizing Multiple Gene Trees Using Cluster Networks. In WABI08, Vol. 5251:296-305 of LNCS, springer, 2008.
Keywords: abstract network, from clusters, from rooted trees, phylogenetic network, phylogeny, polynomial, Program Dendroscope.
Note: http://dx.doi.org/10.1007/978-3-540-87361-7_25, slides from the MIEP Conference available at http://www.lirmm.fr/MIEP08/slides/11_13_rupp.pdf.

Toggle abstract

@InProceedings{RuppHuson2008,
AUTHOR = {Huson, Daniel H. and Rupp, Regula},
TITLE = {Summarizing Multiple Gene Trees Using Cluster Networks},
YEAR = {2008},
BOOKTITLE = {WABI08},
VOLUME = {5251},
PAGES = {296-305},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-540-87361-7_25},
NOTE = {http://dx.doi.org/10.1007/978-3-540-87361-7_25, slides from the MIEP Conference available at http://www.lirmm.fr/MIEP08/slides/11_13_rupp.pdf},
ANNOTE = {BIBUPDATE : 20080605},
KEYWORDS = {abstract network, from clusters, from rooted trees, phylogenetic network, phylogeny, polynomial, Program Dendroscope}
}

22

Lichen Bao and Sergey Bereg. Clustered SplitsNetworks. In COCOA08, Vol. 5165:469-478 of LNCS, springer, 2008.
Keywords: abstract network, from distances, NeighborNet, realization, reconstruction.
Note: http://dx.doi.org/10.1007/978-3-540-85097-7_44, slides available at http://www.utdallas.edu/~besp/cocoa08talk.pdf.

Toggle abstract

@InProceedings{BaoBereg2008,
AUTHOR = {Bao, Lichen and Bereg, Sergey},
TITLE = {Clustered SplitsNetworks},
YEAR = {2008},
BOOKTITLE = {COCOA08},
VOLUME = {5165},
PAGES = {469-478},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-540-85097-7_44},
NOTE = {http://dx.doi.org/10.1007/978-3-540-85097-7_44, slides available at http://www.utdallas.edu/~besp/cocoa08talk.pdf},
ANNOTE = {BIBUPDATE : 20080606},
KEYWORDS = {abstract network, from distances, NeighborNet, realization, reconstruction}
}

23

Birgit Gemeinholzer. Phylogenetic networks. In Björn H. Junker and Falk Schreiber editors, Analysis of Biological Networks, Pages 255-282, John Wiley and Sons Ltd, 2008.
Keywords: survey.
Note: http://www.amazon.com/gp/reader/0470041447/.

@InBook{Gemeinholzer2008,
AUTHOR = {Gemeinholzer, Birgit},
TITLE = {Phylogenetic networks},
YEAR = {2008},
BOOKTITLE = {Analysis of Biological Networks},
PAGES = {255-282},
EDITOR = {Junker, Bj{\~A}�rn H. and Schreiber, Falk},
PUBLISHER = {John Wiley and Sons Ltd},
NOTE = {http://www.amazon.com/gp/reader/0470041447/},
ANNOTE = {CITE : },
KEYWORDS = {survey}
}

24

Victoria Kusherbaeva and Nikolay Vyahhi. Stochastic Approach to Binary Matrix Partitioning for Phylogenetic Networks. In Proceedings of the SYRCODIS 2008 Colloquium on Databases and Information Systems (SYRCoDIS'08), Vol. 355 of CEUR Workshop Proceedings, 2008.
Keywords: clustering, phylogenetic network, phylogeny, reconstruction.
Note: http://ftp.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-355/kusherbaeva.pdf.

@InProceedings{KusherbaevaVyahhi2008,
AUTHOR = {Kusherbaeva, Victoria and Vyahhi, Nikolay},
TITLE = {Stochastic Approach to Binary Matrix Partitioning for Phylogenetic Networks},
YEAR = {2008},
BOOKTITLE = {Proceedings of the SYRCODIS 2008 Colloquium on Databases and Information Systems (SYRCoDIS'08)},
VOLUME = {355},
SERIES = {CEUR Workshop Proceedings},
NOTE = {http://ftp.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-355/kusherbaeva.pdf},
ANNOTE = {CITE : },
KEYWORDS = {clustering, phylogenetic network, phylogeny, reconstruction}
}

25

Sagi Snir and Tamir Tuller. Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. In WABI08, Vol. 5251:354-368 of LNCS, springer, 2008.
Keywords: explicit network, from sequences, HMM, lateral gene transfer, likelihood, phylogenetic network, phylogeny, statistical model.
Note: http://dx.doi.org/10.1007/978-3-540-87361-7_30.

Toggle abstract

@InProceedings{SnirTuller2008,
AUTHOR = {Snir, Sagi and Tuller, Tamir},
TITLE = {Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models},
YEAR = {2008},
BOOKTITLE = {WABI08},
VOLUME = {5251},
PAGES = {354-368},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-540-87361-7_30},
NOTE = {http://dx.doi.org/10.1007/978-3-540-87361-7_30},
ANNOTE = {CITE : },
KEYWORDS = {explicit network, from sequences, HMM, lateral gene transfer, likelihood, phylogenetic network, phylogeny, statistical model}
}

26

Stefan Grünewald, Andreas Spillner, Kristoffer Forslund and Vincent Moulton. Constructing Phylogenetic Supernetworks from Quartets. In WABI08, Vol. 5251:284-295 of LNCS, springer, 2008.
Keywords: abstract network, from quartets, from unrooted trees, phylogenetic network, phylogeny, Program QNet, Program SplitsTree, reconstruction, split network.
Note: http://dx.doi.org/10.1007/978-3-540-87361-7_24.

Toggle abstract

@InProceedings{GSFM2008,
AUTHOR = {Gr{\~A}�newald, Stefan and Spillner, Andreas and Forslund, Kristoffer and Moulton, Vincent},
TITLE = {Constructing Phylogenetic Supernetworks from Quartets},
YEAR = {2008},
BOOKTITLE = {WABI08},
VOLUME = {5251},
PAGES = {284-295},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-540-87361-7_24},
NOTE = {http://dx.doi.org/10.1007/978-3-540-87361-7_24},
ANNOTE = {CITE : },
KEYWORDS = {abstract network, from quartets, from unrooted trees, phylogenetic network, phylogeny, Program QNet, Program SplitsTree, reconstruction, split network}
}

27

Gabriel Cardona, Mercè Llabrés, Francesc Rosselló and Gabriel Valiente. Phylogenetic Networks: Justification, Models, Distances and Algorithms. In VI Jornadas de Matemática Discreta y Algorítmica (JMDA'08), 2008.
Keywords: distance between networks, mu distance, phylogenetic network, phylogeny, polynomial, survey, time consistent network, tree-child network, tripartition distance, triplet distance.
Note: http://bioinfo.uib.es/media/uploaded/jmda2008_submission_61-1.pdf.

@InProceedings{CLRV2008e,
AUTHOR = {Cardona, Gabriel and Llabr{\~A}�s, Merc{\~A}� and Rossell{\~A}�, Francesc and Valiente, Gabriel},
TITLE = {Phylogenetic Networks: Justification, Models, Distances and Algorithms},
YEAR = {2008},
BOOKTITLE = {VI Jornadas de Matem{\~A}�tica Discreta y Algor{\~A}�tmica (JMDA'08)},
NOTE = {http://bioinfo.uib.es/media/uploaded/jmda2008_submission_61-1.pdf},
ANNOTE = {BIBUPDATE : 20080725},
KEYWORDS = {distance between networks, mu distance, phylogenetic network, phylogeny, polynomial, survey, time consistent network, tree-child network, tripartition distance, triplet distance}
}

28

Cuong Than, Derek Ruths and Luay Nakhleh. PhyloNet: A Software Package for Analyzing and Reconstructing Reticulate Evolutionary Relationships. In BMCB, Vol. 9(322), 2008.
Keywords: Program PhyloNet, software.
Note: http://dx.doi.org/10.1186/1471-2105-9-322.

Toggle abstract

@Article{TRN2008,
AUTHOR = {Than, Cuong and Ruths, Derek and Nakhleh, Luay},
TITLE = {PhyloNet: A Software Package for Analyzing and Reconstructing Reticulate Evolutionary Relationships},
YEAR = {2008},
JOURNAL = {BMCB},
VOLUME = {9},
NUMBER = {322},
URL = {http://dx.doi.org/10.1186/1471-2105-9-322},
NOTE = {http://dx.doi.org/10.1186/1471-2105-9-322},
ANNOTE = {BIBUPDATE : 20080731},
KEYWORDS = {Program PhyloNet, software}
}

29

Iyad A. Kanj, Luay Nakhleh, Cuong Than and Ge Xia. Seeing the Trees and Their Branches in the Network is Hard. In TCS, Vol. 401:153-164, 2008.
Keywords: evaluation, from network, from rooted trees, NP complete, phylogenetic network, phylogeny, tree containment.
Note: http://www.cs.rice.edu/~nakhleh/Papers/tcs08.pdf.

@Article{KNTX2008,
AUTHOR = {Kanj, Iyad A. and Nakhleh, Luay and Than, Cuong and Xia, Ge},
TITLE = {Seeing the Trees and Their Branches in the Network is Hard},
YEAR = {2008},
JOURNAL = {TCS},
VOLUME = {401},
PAGES = {153-164},
URL = {http://dx.doi.org/10.1016/j.tcs.2008.04.019},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/tcs08.pdf},
ANNOTE = {BIBUPDATE : },
KEYWORDS = {evaluation, from network, from rooted trees, NP complete, phylogenetic network, phylogeny, tree containment}
}

30

Barbara R. Holland, Steffi Benthin, Peter J. Lockhart, Vincent Moulton and Katharina Huber. Using supernetworks to distinguish hybridization from lineage-sorting. In BMCEB, Vol. 8(202), 2008.
Keywords: explicit network, from unrooted trees, hybridization, lineage sorting, phylogenetic network, phylogeny, reconstruction, supernetwork.
Note: http://dx.doi.org/10.1186/1471-2148-8-202.

Toggle abstract

@Article{HBLMH2008,
AUTHOR = {Holland, Barbara R. and Benthin, Steffi and Lockhart, Peter J. and Moulton, Vincent and Huber, Katharina},
TITLE = {Using supernetworks to distinguish hybridization from lineage-sorting},
YEAR = {2008},
JOURNAL = {BMCEB},
VOLUME = {8},
NUMBER = {202},
URL = {http://dx.doi.org/10.1186/1471-2148-8-202},
NOTE = {http://dx.doi.org/10.1186/1471-2148-8-202},
ANNOTE = {BIBUPDATE : 20080816},
KEYWORDS = {explicit network, from unrooted trees, hybridization, lineage sorting, phylogenetic network, phylogeny, reconstruction, supernetwork}
}

31

Wing-Kin Sung. Constructing a Galled Phylogenetic Network. In Ming-Yang Kao editor, Encyclopedia of Algorithms, Springer Reference, 2008.
Keywords: explicit network, from triplets, galled tree, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1007/978-0-387-30162-4_92.

@InBook{Sung2008,
AUTHOR = {Sung, Wing-Kin},
TITLE = {Constructing a Galled Phylogenetic Network},
YEAR = {2008},
BOOKTITLE = {Encyclopedia of Algorithms},
EDITOR = {Kao, Ming-Yang},
PUBLISHER = {Springer Reference},
URL = {http://dx.doi.org/10.1007/978-0-387-30162-4_92},
NOTE = {http://dx.doi.org/10.1007/978-0-387-30162-4_92},
ANNOTE = {BIBUPDATE : 20080925},
KEYWORDS = {explicit network, from triplets, galled tree, phylogenetic network, phylogeny, reconstruction}
}

32

Ernst Althaus and Rouven Naujoks. Reconstructing Phylogenetic Networks with One Recombination. In Proceedings of the seventh International Workshop on Experimental Algorithms (WEA'08), Vol. 5038:275-288 of LNCS, springer, 2008.
Keywords: enumeration, explicit network, exponential algorithm, from sequences, generation, parsimony, phylogenetic network, phylogeny, reconstruction, unicyclic network.
Note: http://dx.doi.org/10.1007/978-3-540-68552-4_21.

Toggle abstract

@InProceedings{AlthausNaujoks2008,
AUTHOR = {Althaus, Ernst and Naujoks, Rouven},
TITLE = {Reconstructing Phylogenetic Networks with One Recombination},
YEAR = {2008},
BOOKTITLE = {Proceedings of the seventh International Workshop on Experimental Algorithms (WEA'08)},
VOLUME = {5038},
PAGES = {275-288},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-540-68552-4_21},
NOTE = {http://dx.doi.org/10.1007/978-3-540-68552-4_21},
ANNOTE = {CITE : },
KEYWORDS = {enumeration, explicit network, exponential algorithm, from sequences, generation, parsimony, phylogenetic network, phylogeny, reconstruction, unicyclic network}
}

33

Miguel Arenas, Gabriel Valiente and David Posada. Characterization of reticulate networks based on the coalescent with recombination. In MBE, Vol. 25(12):2517-2520, 2008.
Keywords: coalescent, evaluation, explicit network, galled tree, phylogenetic network, phylogeny, Program Recodon, regular network, simulation, tree sibling network, tree-child network.
Note: http://dx.doi.org/10.1093/molbev/msn219.

Toggle abstract

@Article{AVP2008,
AUTHOR = {Arenas, Miguel and Valiente, Gabriel and Posada, David},
TITLE = {Characterization of reticulate networks based on the coalescent with recombination},
YEAR = {2008},
JOURNAL = {MBE},
VOLUME = {25},
NUMBER = {12},
PAGES = {2517-2520},
URL = {http://dx.doi.org/10.1093/molbev/msn219},
NOTE = {http://dx.doi.org/10.1093/molbev/msn219},
ANNOTE = {BIBUPDATE : 20081001},
KEYWORDS = {coalescent, evaluation, explicit network, galled tree, phylogenetic network, phylogeny, Program Recodon, regular network, simulation, tree sibling network, tree-child network}
}

34

Gabriel Cardona, Francesc Rosselló and Gabriel Valiente. Extended Newick: It is Time for a Standard Representation. In BMCB, Vol. 9:532, 2008.
Keywords: evaluation, explicit network, phylogenetic network, Program Bio PhyloNetwork, Program Dendroscope, Program NetGen, Program PhyloNet, Program SplitsTree, Program TCS, visualization.
Note: http://bioinfo.uib.es/media/uploaded/bmc-2008-enewick-sub.pdf.

@Article{CRV2008c,
AUTHOR = {Cardona, Gabriel and Rossell{\~A}�, Francesc and Valiente, Gabriel},
TITLE = {Extended Newick: It is Time for a Standard Representation},
YEAR = {2008},
JOURNAL = {BMCB},
VOLUME = {9},
PAGES = {532},
URL = {http://dx.doi.org/10.1186/1471-2105-9-532},
NOTE = {http://bioinfo.uib.es/media/uploaded/bmc-2008-enewick-sub.pdf},
ANNOTE = {BIBUPDATE : 20081011, 20081216},
KEYWORDS = {evaluation, explicit network, phylogenetic network, Program Bio PhyloNetwork, Program Dendroscope, Program NetGen, Program PhyloNet, Program SplitsTree, Program TCS, visualization}
}

35

Supriya Munshaw and Thomas B. Kepler. An Information-Theoretic Method for the Treatment of Plural Ancestry in Phylogenetics. In MBE, Vol. 25(6):1199-1208, 2008.
Keywords: explicit network, from sequences, heuristic, phylogenetic network, reconstruction, simulated annealing, software.
Note: http://dx.doi.org/10.1093/molbev/msn066.

Toggle abstract

@Article{MunshawKepler2008,
AUTHOR = {Munshaw, Supriya and Kepler, Thomas B.},
TITLE = {An Information-Theoretic Method for the Treatment of Plural Ancestry in Phylogenetics},
YEAR = {2008},
JOURNAL = {MBE},
VOLUME = {25},
NUMBER = {6},
PAGES = {1199-1208},
URL = {http://dx.doi.org/10.1093/molbev/msn066},
NOTE = {http://dx.doi.org/10.1093/molbev/msn066},
ANNOTE = {CITE : },
KEYWORDS = {explicit network, from sequences, heuristic, phylogenetic network, reconstruction, simulated annealing, software}
}

36

Miguel Arenas and David Posada. Recodon: Coalescent simulation of coding DNA sequences with recombination, migration and demography. In BMCB, Vol. 8(458), 2008.
Keywords: coalescent, generation, Program Recodon, software.
Note: http://dx.doi.org/10.1186/1471-2105-8-458.

Toggle abstract

@Article{ArenasPosada2007,
AUTHOR = {Arenas, Miguel and Posada, David},
TITLE = {Recodon: Coalescent simulation of coding DNA sequences with recombination, migration and demography},
YEAR = {2008},
JOURNAL = {BMCB},
VOLUME = {8},
NUMBER = {458},
URL = {http://dx.doi.org/10.1186/1471-2105-8-458},
NOTE = {http://dx.doi.org/10.1186/1471-2105-8-458},
ANNOTE = {BIBUPDATE : 20081020},
KEYWORDS = {coalescent, generation, Program Recodon, software}
}

37

Cuong Than, Guohua Jin and Luay Nakhleh. Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer. In Proceedings of the Sixth RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG'08), Vol. 5267:113-127 of LNCS, springer, 2008.
Keywords: bootstrap, explicit network, from rooted trees, from sequences, lateral gene transfer, phylogenetic network, phylogeny, Program Nepal, Program PhyloNet, reconstruction.
Note: http://www.cs.rice.edu/~nakhleh/Papers/recombcg-08.pdf, slides available at http://igm.univ-mlv.fr/RCG08/RCG08slides/Cuong_Than_RCG08.pdf.

@InProceedings{TJN2008,
AUTHOR = {Than, Cuong and Jin, Guohua and Nakhleh, Luay},
TITLE = {Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer},
YEAR = {2008},
BOOKTITLE = {Proceedings of the Sixth RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG'08)},
VOLUME = {5267},
PAGES = {113-127},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-540-87989-3_9},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/recombcg-08.pdf, slides available at http://igm.univ-mlv.fr/RCG08/RCG08slides/Cuong_Than_RCG08.pdf},
ANNOTE = {BIBUPDATE : },
KEYWORDS = {bootstrap, explicit network, from rooted trees, from sequences, lateral gene transfer, phylogenetic network, phylogeny, Program Nepal, Program PhyloNet, reconstruction}
}

38

Anthony Labarre. Combinatorial aspects of genome rearrangements and haplotype networks. PhD thesis, Université Libre de Bruxelles, Belgium, 2008.
Keywords: abstract network, from unrooted trees, haplotype network, phylogenetic network, phylogeny, reconstruction.
Note: http://homepages.ulb.ac.be/~alabarre/publications/phd-thesis.pdf.

@PhdThesis{Labarre2008,
AUTHOR = {Labarre, Anthony},
TITLE = {Combinatorial aspects of genome rearrangements and haplotype networks},
YEAR = {2008},
SCHOOL = {Universit{\~A}� Libre de Bruxelles, Belgium},
NOTE = {http://homepages.ulb.ac.be/~alabarre/publications/phd-thesis.pdf},
ANNOTE = {CITE : },
KEYWORDS = {abstract network, from unrooted trees, haplotype network, phylogenetic network, phylogeny, reconstruction}
}

39

Hadas Birin, Zohar Gal-Or, Isaac Elias and Tamir Tuller. Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion. In BIO, Vol. 24(6):826-832, 2008.
Note: http://dx.doi.org/10.1093/bioinformatics/btn024.

Toggle abstract

@Article{BGET2008,
AUTHOR = {Birin, Hadas and Gal-Or, Zohar and Elias, Isaac and Tuller, Tamir},
TITLE = {Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion},
YEAR = {2008},
JOURNAL = {BIO},
VOLUME = {24},
NUMBER = {6},
PAGES = {826-832},
URL = {http://dx.doi.org/10.1093/bioinformatics/btn024},
NOTE = {http://dx.doi.org/10.1093/bioinformatics/btn024}
}

40

Jaroslaw Byrka. Randomized Approximation Algorithms: Facility Location, Phylogenetic Networks, Nash Equilibria. PhD thesis, Eindhoven University of Technology, Netherlands, 2008.
Note: http://disopt.epfl.ch/webdav/site/disopt/users/191068/public/phdthesis_byrka.pdf.

@PhdThesis{Byrka2008,
AUTHOR = {Byrka, Jaroslaw},
TITLE = {Randomized Approximation Algorithms: Facility Location, Phylogenetic Networks, Nash Equilibria},
YEAR = {2008},
SCHOOL = {Eindhoven University of Technology, Netherlands},
NOTE = {http://disopt.epfl.ch/webdav/site/disopt/users/191068/public/phdthesis_byrka.pdf}
}

41

Tal Dagan, Yael Artzy-Randrup and William Martin. Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. In PNAS, Vol. 105:10039-10044, 2008.
Keywords: from sequences, from species tree, heuristic, lateral gene transfer, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1073/pnas.0800679105.

Toggle abstract

@Article{DAM2008,
AUTHOR = {Dagan, Tal and Artzy-Randrup, Yael and Martin, William},
TITLE = {Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution},
YEAR = {2008},
JOURNAL = {PNAS},
VOLUME = {105},
PAGES = {10039-10044},
URL = {http://dx.doi.org/10.1073/pnas.0800679105},
NOTE = {http://dx.doi.org/10.1073/pnas.0800679105},
KEYWORDS = {from sequences, from species tree, heuristic, lateral gene transfer, phylogenetic network, phylogeny, reconstruction}
}

2007

1

Magnus Bordewich, Simone Linz, Katherine St. John and Charles Semple. A reduction algorithm for computing the hybridization number of two trees. In EBIO, Vol. 3:86-98, 2007.
Keywords: agreement forest, FPT, from rooted trees, hybridization, phylogenetic network, phylogeny, Program HybridNumber.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BLSS07.pdf.

@Article{BLSS2007,
AUTHOR = {Bordewich, Magnus and Linz, Simone and St. John, Katherine and Semple, Charles},
TITLE = {A reduction algorithm for computing the hybridization number of two trees},
YEAR = {2007},
JOURNAL = {EBIO},
VOLUME = {3},
PAGES = {86-98},
URL = {http://www.ncbi.nlm.nih.gov/pubmed/19461978},
NOTE = {http://www.math.canterbury.ac.nz/~c.semple/papers/BLSS07.pdf},
ANNOTE = {BIBUPDATE : 20070919},
KEYWORDS = {agreement forest, FPT, from rooted trees, hybridization, phylogenetic network, phylogeny, Program HybridNumber}
}

2

Magnus Bordewich and Charles Semple. Computing the minimum number of hybridization events for a consistent evolutionary history. In DAM, Vol. 155:914-918, 2007.
Keywords: agreement forest, approximation, APX hard, explicit network, from rooted trees, hybridization, inapproximability, NP complete, phylogenetic network, phylogeny, SPR distance.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BS06a.pdf.

@Article{BordewichSemple2007a,
AUTHOR = {Bordewich, Magnus and Semple, Charles},
TITLE = {Computing the minimum number of hybridization events for a consistent evolutionary history},
YEAR = {2007},
JOURNAL = {DAM},
VOLUME = {155},
PAGES = {914-918},
URL = {http://dx.doi.org/10.1016/j.dam.2006.08.008},
NOTE = {http://www.math.canterbury.ac.nz/~c.semple/papers/BS06a.pdf},
ANNOTE = {BIBUPDATE : 20070919},
KEYWORDS = {agreement forest, approximation, APX hard, explicit network, from rooted trees, hybridization, inapproximability, NP complete, phylogenetic network, phylogeny, SPR distance}
}

3

Magnus Bordewich and Charles Semple. Computing the hybridization number of two phylogenetic trees is fixed-parameter tractable. In TCBB, Vol. 4(3):458-466, 2007.
Keywords: FPT, hybridization.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BS06b.pdf.

@Article{BordewichSemple2007b,
AUTHOR = {Bordewich, Magnus and Semple, Charles},
TITLE = {Computing the hybridization number of two phylogenetic trees is fixed-parameter tractable},
YEAR = {2007},
JOURNAL = {TCBB},
VOLUME = {4},
NUMBER = {3},
PAGES = {458-466},
URL = {http://dx.doi.org/10.1016/j.dam.2006.08.008},
NOTE = {http://www.math.canterbury.ac.nz/~c.semple/papers/BS06b.pdf},
ANNOTE = {BIBUPDATE : 20070919},
KEYWORDS = {FPT, hybridization}
}

4

Olivier Gauthier and François-Joseph Lapointe. Hybrids and Phylogenetics Revisited: A Statistical Test of Hybridization Using Quartets. In Systematic Botany, Vol. 32(1):8-15, 2007.
Keywords: explicit network, from quartets, hybridization, phylogenetic network, phylogeny, reconstruction, reticulogram, split decomposition.
Note: http://dx.doi.org/10.1600/036364407780360238.

Toggle abstract

@Article{GauthierLapointe2007a,
AUTHOR = {Gauthier, Olivier and Lapointe, Fran{\~A}�ois-Joseph},
TITLE = {Hybrids and Phylogenetics Revisited: A Statistical Test of Hybridization Using Quartets},
YEAR = {2007},
JOURNAL = {Systematic Botany},
VOLUME = {32},
NUMBER = {1},
PAGES = {8-15},
URL = {http://dx.doi.org/10.1600/036364407780360238},
NOTE = {http://dx.doi.org/10.1600/036364407780360238},
ANNOTE = {CITE : },
KEYWORDS = {explicit network, from quartets, hybridization, phylogenetic network, phylogeny, reconstruction, reticulogram, split decomposition}
}

5

Olivier Gauthier and François-Joseph Lapointe. Seeing the Trees for the Network: Consensus, Information Content, and Superphylogenies. In Systematic Biology, Vol. 56(2):345-355, 2007.
Keywords: consensus.
Note: http://dx.doi.org/10.1080/10635150701286549.

Toggle abstract [No abstract available]

@Article{GauthierLapointe2007b,
AUTHOR = {Gauthier, Olivier and Lapointe, Fran{\~A}�ois-Joseph},
TITLE = {Seeing the Trees for the Network: Consensus, Information Content, and Superphylogenies},
YEAR = {2007},
JOURNAL = {Systematic Biology},
VOLUME = {56},
NUMBER = {2},
PAGES = {345-355},
URL = {http://dx.doi.org/10.1080/10635150701286549},
NOTE = {http://dx.doi.org/10.1080/10635150701286549},
ANNOTE = {CITE : },
KEYWORDS = {consensus}
}

6

Stefan Grünewald, Kristoffer Forslund, Andreas W. M. Dress and Vincent Moulton. QNet: An agglomerative method for the construction of phylogenetic networks from weighted quartets. In MBE, Vol. 24(2):532-538, 2007.
Keywords: abstract network, circular split system, from quartets, phylogenetic network, phylogeny, Program QNet, reconstruction, software.
Note: http://mbe.oxfordjournals.org/cgi/content/abstract/24/2/532.

Toggle abstract

@Article{GFDM2007,
AUTHOR = {Gr{\~A}�newald, Stefan and Forslund, Kristoffer and Dress, Andreas W. M. and Moulton, Vincent},
TITLE = {QNet: An agglomerative method for the construction of phylogenetic networks from weighted quartets},
YEAR = {2007},
JOURNAL = {MBE},
VOLUME = {24},
NUMBER = {2},
PAGES = {532-538},
URL = {http://dx.doi.org/10.1093/molbev/msl180},
NOTE = {http://mbe.oxfordjournals.org/cgi/content/abstract/24/2/532},
ANNOTE = {CITE : },
KEYWORDS = {abstract network, circular split system, from quartets, phylogenetic network, phylogeny, Program QNet, reconstruction, software}
}

7

Dan Gusfield, Dean Hickerson and Satish Eddhu. An efficiently computed lower bound on the number of recombinations in phylogenetic networks: Theory and empirical study. In DAM, Vol. 155(6-7):806-830, 2007.
Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/cclowerbound.pdf.

Toggle abstract

@Article{GHE2007,
AUTHOR = {Gusfield, Dan and Hickerson, Dean and Eddhu, Satish},
TITLE = {An efficiently computed lower bound on the number of recombinations in phylogenetic networks: Theory and empirical study},
YEAR = {2007},
JOURNAL = {DAM},
VOLUME = {155},
NUMBER = {6-7},
PAGES = {806-830},
URL = {http://dx.doi.org/10.1016/j.dam.2005.05.044},
NOTE = {http://wwwcsif.cs.ucdavis.edu/~gusfield/cclowerbound.pdf},
ANNOTE = {BIBUPDATE : 20070914}
}

8

Barbara R. Holland, Glenn Conner, Katharina Huber and Vincent Moulton. Imputing Supertrees and Supernetworks from Quartets. In Systematic Biology, Vol. 56(1):57-67, 2007.
Keywords: abstract network, from unrooted trees, phylogenetic network, phylogeny, Program Quartet, reconstruction, split network, supernetwork.
Note: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.99.3215.

Toggle abstract

@Article{HCHM2007,
AUTHOR = {Holland, Barbara R. and Conner, Glenn and Huber, Katharina and Moulton, Vincent},
TITLE = {Imputing Supertrees and Supernetworks from Quartets},
YEAR = {2007},
JOURNAL = {Systematic Biology},
VOLUME = {56},
NUMBER = {1},
PAGES = {57-67},
URL = {http://dx.doi.org/10.1080/10635150601167013},
NOTE = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.99.3215},
ANNOTE = {BIBUPDATE : 20070918},
KEYWORDS = {abstract network, from unrooted trees, phylogenetic network, phylogeny, Program Quartet, reconstruction, split network, supernetwork}
}

9

Katharina Huber, Bengt Oxelman, Martin Lott and Vincent Moulton. Reconstructing the Evolutionary History of Polyploids from Multilabeled Trees. In MBE, Vol. 23(9):1784-1791, 2007.
Keywords: duplication, explicit network, from multilabeled tree, from trees, phylogenetic network, phylogeny, Program PADRE, reconstruction, software.
Note: http://mbe.oxfordjournals.org/cgi/content/full/23/9/1784.

Toggle abstract

@Article{HOLM2006,
AUTHOR = {Huber, Katharina and Oxelman, Bengt and Lott, Martin and Moulton, Vincent},
TITLE = {Reconstructing the Evolutionary History of Polyploids from Multilabeled Trees},
YEAR = {2007},
JOURNAL = {MBE},
VOLUME = {23},
NUMBER = {9},
PAGES = {1784-1791},
URL = {http://dx.doi.org/10.1093/molbev/msl045},
NOTE = {http://mbe.oxfordjournals.org/cgi/content/full/23/9/1784},
ANNOTE = {BIBUPDATE : 20071002},
KEYWORDS = {duplication, explicit network, from multilabeled tree, from trees, phylogenetic network, phylogeny, Program PADRE, reconstruction, software}
}

10

Daniel H. Huson. Split networks and Reticulate Networks. In Olivier Gascuel and Mike Steel editors, Reconstructing Evolution, New Mathematical and Computational Advances, Pages 247-276, Oxford University Press, 2007.
Keywords: abstract network, consensus, from rooted trees, from sequences, from splits, from unrooted trees, galled tree, hybridization, phylogenetic network, phylogeny, Program Beagle, Program Spectronet, Program SplitsTree, Program SPNet, recombination, reconstruction, split network, survey.
Note: similar to http://www-ab.informatik.uni-tuebingen.de/research/phylonets/GCB2006.pdf.

@InBook{Huson2007a,
AUTHOR = {Huson, Daniel H.},
TITLE = {Split networks and Reticulate Networks},
YEAR = {2007},
BOOKTITLE = {Reconstructing Evolution, New Mathematical and Computational Advances},
PAGES = {247-276},
EDITOR = {Gascuel, Olivier and Steel, Mike},
PUBLISHER = {Oxford University Press},
NOTE = {similar to http://www-ab.informatik.uni-tuebingen.de/research/phylonets/GCB2006.pdf},
ANNOTE = {CITE : },
KEYWORDS = {abstract network, consensus, from rooted trees, from sequences, from splits, from unrooted trees, galled tree, hybridization, phylogenetic network, phylogeny, Program Beagle, Program Spectronet, Program SplitsTree, Program SPNet, recombination, reconstruction, split network, survey}
}

11

Daniel H. Huson and Tobias Kloepper. Beyond Galled Trees - Decomposition and Computation of Galled Networks. In RECOMB07, Vol. 4453:211-225 of LNCS, springer, 2007.
Keywords: FPT, from splits, from trees, galled network, phylogenetic network, phylogeny, Program SplitsTree, reconstruction.
Note: http://dx.doi.org/10.1007/978-3-540-71681-5_15, errata..

@InProceedings{HusonKloepper2007,
AUTHOR = {Huson, Daniel H. and Kloepper, Tobias},
TITLE = {Beyond Galled Trees - Decomposition and Computation of Galled Networks},
YEAR = {2007},
BOOKTITLE = {RECOMB07},
VOLUME = {4453},
PAGES = {211-225},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-540-71681-5_15},
NOTE = {http://dx.doi.org/10.1007/978-3-540-71681-5_15, errata.},
ANNOTE = {CITE : },
KEYWORDS = {FPT, from splits, from trees, galled network, phylogenetic network, phylogeny, Program SplitsTree, reconstruction}
}

12

Guohua Jin, Luay Nakhleh, Sagi Snir and Tamir Tuller. Efficient Parsimony-based Methods for Phylogenetic Network Reconstruction. In ECCB06, Vol. 23(2):e123-e128 of BIO, 2007.
Keywords: parsimony, phylogenetic network, phylogeny, Program Nepal, reconstruction.
Note: http://www.cs.rice.edu/~nakhleh/Papers/eccb06.pdf.

@InProceedings{JNST2007,
AUTHOR = {Jin, Guohua and Nakhleh, Luay and Snir, Sagi and Tuller, Tamir},
TITLE = {Efficient Parsimony-based Methods for Phylogenetic Network Reconstruction},
YEAR = {2007},
BOOKTITLE = {ECCB06},
VOLUME = {23(2)},
PAGES = {e123-e128},
SERIES = {BIO},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl313},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/eccb06.pdf},
ANNOTE = {BIBUPDATE : 20070917},
KEYWORDS = {parsimony, phylogenetic network, phylogeny, Program Nepal, reconstruction}
}

13

Guohua Jin, Luay Nakhleh, Sagi Snir and Tamir Tuller. A New Linear-time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance. In ISBRA07, Vol. 4463:61-72 of LNCS, springer, 2007.
Keywords: approximation, heuristic, parsimony, phylogenetic network, phylogeny, Program Nepal.
Note: http://www.cs.rice.edu/~nakhleh/Papers/isbra07.pdf.

@InProceedings{JNST2007a,
AUTHOR = {Jin, Guohua and Nakhleh, Luay and Snir, Sagi and Tuller, Tamir},
TITLE = {A New Linear-time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance},
YEAR = {2007},
BOOKTITLE = {ISBRA07},
VOLUME = {4463},
PAGES = {61-72},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-540-72031-7_6},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/isbra07.pdf},
ANNOTE = {BIBUPDATE : 20070917},
KEYWORDS = {approximation, heuristic, parsimony, phylogenetic network, phylogeny, Program Nepal}
}

14

Guohua Jin, Luay Nakhleh, Sagi Snir and Tamir Tuller. Inferring Phylogenetic Networks by the Maximum Parsimony Criterion: A Case Study. In MBE, Vol. 24(1):324-337, 2007.
Keywords: explicit network, parsimony, phylogenetic network, phylogeny, Program Nepal, reconstruction.
Note: http://www.cs.rice.edu/~nakhleh/Papers/MBE06.pdf.

@Article{JNST2007b,
AUTHOR = {Jin, Guohua and Nakhleh, Luay and Snir, Sagi and Tuller, Tamir},
TITLE = {Inferring Phylogenetic Networks by the Maximum Parsimony Criterion: A Case Study},
YEAR = {2007},
JOURNAL = {MBE},
VOLUME = {24},
NUMBER = {1},
PAGES = {324-337},
URL = {http://dx.doi.org/10.1093/molbev/msl163},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/MBE06.pdf},
ANNOTE = {BIBUPDATE : 20070917},
KEYWORDS = {explicit network, parsimony, phylogenetic network, phylogeny, Program Nepal, reconstruction}
}

15

Iyad A. Kanj, Luay Nakhleh, Cuong Than and Ge Xia. Seeing the Trees and Their Branches in the Network is Hard. In Proceedings of the Tenth Italian Conference on Theoretical Computer Science (ICTCS'07), 2007.
Keywords: evaluation, from network, from rooted trees, NP complete, phylogenetic network, phylogeny, tree containment.
Note: http://www.cs.rice.edu/~nakhleh/Papers/ictcs07.pdf.

@InProceedings{KNTX2007,
AUTHOR = {Kanj, Iyad A. and Nakhleh, Luay and Than, Cuong and Xia, Ge},
TITLE = {Seeing the Trees and Their Branches in the Network is Hard},
YEAR = {2007},
BOOKTITLE = {Proceedings of the Tenth Italian Conference on Theoretical Computer Science (ICTCS'07)},
URL = {http://dx.doi.org/10.1142/9789812770998_0011},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/ictcs07.pdf},
ANNOTE = {BIBUPDATE : },
KEYWORDS = {evaluation, from network, from rooted trees, NP complete, phylogenetic network, phylogeny, tree containment}
}

16

Cam Thach Nguyen, Nguyen Bao Nguyen and Wing-Kin Sung. Fast Algorithms for computing the Tripartition-based Distance between Phylogenetic Networks. In JCO, Vol. 13(3), 2007.
Keywords: distance between networks, phylogenetic network, phylogeny, tripartition distance.
Note: http://dx.doi.org/10.1007/s10878-006-9025-5.

Toggle abstract

@Article{NNS2007,
AUTHOR = {Nguyen, Cam Thach and Nguyen, Nguyen Bao and Sung, Wing-Kin},
TITLE = {Fast Algorithms for computing the Tripartition-based Distance between Phylogenetic Networks},
YEAR = {2007},
JOURNAL = {JCO},
VOLUME = {13},
NUMBER = {3},
URL = {http://dx.doi.org/10.1007/s10878-006-9025-5},
NOTE = {http://dx.doi.org/10.1007/s10878-006-9025-5},
ANNOTE = {BIBUPDATE : 20071118},
KEYWORDS = {distance between networks, phylogenetic network, phylogeny, tripartition distance}
}

17

Cam Thach Nguyen, Nguyen Bao Nguyen, Wing-Kin Sung and Louxin Zhang. Reconstructing Recombination Network from Sequence Data: The Small Parsimony Problem. In TCBB, Vol. 4(3):394-402, 2007.
Keywords: explicit network, from sequences, labeling, NP complete, parsimony, phylogenetic network, phylogeny.
Note: http://www.cs.washington.edu/homes/ncthach/Papers/TCBB2007.pdf.

@Article{NNSZ2007,
AUTHOR = {Nguyen, Cam Thach and Nguyen, Nguyen Bao and Sung, Wing-Kin and Zhang, Louxin},
TITLE = {Reconstructing Recombination Network from Sequence Data: The Small Parsimony Problem},
YEAR = {2007},
JOURNAL = {TCBB},
VOLUME = {4},
NUMBER = {3},
PAGES = {394-402},
URL = {http://dx.doi.org/10.1109/tcbb.2007.1018},
NOTE = {http://www.cs.washington.edu/homes/ncthach/Papers/TCBB2007.pdf},
ANNOTE = {BIBUPDATE : 20071118},
KEYWORDS = {explicit network, from sequences, labeling, NP complete, parsimony, phylogenetic network, phylogeny}
}

18

Charles Semple. Hybridization Networks. In Olivier Gascuel and Mike Steel editors, Reconstructing Evolution, New Mathematical and Computational Advances, Pages 277-314, Oxford University Press, 2007.
Keywords: hybridization, phylogenetic network, phylogeny, recombination.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/S06.pdf.

@InBook{Semple2007,
AUTHOR = {Semple, Charles},
TITLE = {Hybridization Networks},
YEAR = {2007},
BOOKTITLE = {Reconstructing Evolution, New Mathematical and Computational Advances},
PAGES = {277-314},
EDITOR = {Gascuel, Olivier and Steel, Mike},
PUBLISHER = {Oxford University Press},
NOTE = {http://www.math.canterbury.ac.nz/~c.semple/papers/S06.pdf},
ANNOTE = {BIBUPDATE : 20070919},
KEYWORDS = {hybridization, phylogenetic network, phylogeny, recombination}
}

19

Stephen J. Willson. Unique determination of some homoplasies at hybridization events. In BMB, Vol. 69(5):1709-1725, 2007.
Keywords: explicit network, from network, hybridization, labeling, normal network, phylogenetic network, tree-child network.
Note: http://www.public.iastate.edu/~swillson/unique.det.pdf.

@Article{Willson2007a,
AUTHOR = {Willson, Stephen J.},
TITLE = {Unique determination of some homoplasies at hybridization events},
YEAR = {2007},
JOURNAL = {BMB},
VOLUME = {69},
NUMBER = {5},
PAGES = {1709-1725},
URL = {http://dx.doi.org/10.1007/s11538-006-9187-4},
NOTE = {http://www.public.iastate.edu/~swillson/unique.det.pdf},
ANNOTE = {BIBUPDATE : 20071216},
KEYWORDS = {explicit network, from network, hybridization, labeling, normal network, phylogenetic network, tree-child network}
}

20

Stephen J. Willson. Reconstruction of Some Hybrid Phylogenetic Networks with Homoplasies from Distances. In BMB, Vol. 69(8):2561-2590, 2007.
Keywords: explicit network, from distances, normal network, phylogenetic network, phylogeny, reconstruction.
Note: http://www.public.iastate.edu/~swillson/BMB06-97.willson.pdf.

@Article{Willson2007c,
AUTHOR = {Willson, Stephen J.},
TITLE = {Reconstruction of Some Hybrid Phylogenetic Networks with Homoplasies from Distances},
YEAR = {2007},
JOURNAL = {BMB},
VOLUME = {69},
NUMBER = {8},
PAGES = {2561-2590},
URL = {http://dx.doi.org/10.1007/s11538-007-9232-y},
NOTE = {http://www.public.iastate.edu/~swillson/BMB06-97.willson.pdf},
ANNOTE = {BIBUPDATE : 20071216},
KEYWORDS = {explicit network, from distances, normal network, phylogenetic network, phylogeny, reconstruction}
}

21

Yufeng Wu and Dan Gusfield. Efficient Computation of Minimum Recombination with Genotypes (not Haplotypes) In JBCB, Vol. 5(2(a)):181-200, 2007.
Note: http://dx.doi.org/10.1142/S0219720007002631.

@Article{WuGusfield2007a,
AUTHOR = {Wu, Yufeng and Gusfield, Dan},
TITLE = {Efficient Computation of Minimum Recombination with Genotypes (not Haplotypes)},
YEAR = {2007},
JOURNAL = {JBCB},
VOLUME = {5},
NUMBER = {2(a)},
PAGES = {181-200},
URL = {http://dx.doi.org/10.1142/S0219720007002631},
NOTE = {http://dx.doi.org/10.1142/S0219720007002631},
ANNOTE = {CITE : }
}

22

Yufeng Wu and Dan Gusfield. Improved Algorithms for Inferring the Minimum Mosaic of a Set of Recombinants. In CPM07, Vol. 4580:150-161 of LNCS, springer, 2007.
Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/CPM2007mosaic.pdf.

@InProceedings{WuGusfield2007b,
AUTHOR = {Wu, Yufeng and Gusfield, Dan},
TITLE = {Improved Algorithms for Inferring the Minimum Mosaic of a Set of Recombinants},
YEAR = {2007},
BOOKTITLE = {CPM07},
VOLUME = {4580},
PAGES = {150-161},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-540-73437-6_17},
NOTE = {http://wwwcsif.cs.ucdavis.edu/~gusfield/CPM2007mosaic.pdf},
ANNOTE = {BIBUPDATE : 20070918}
}

23

Yufeng Wu and Dan Gusfield. A new recombination lower bound and the minimum perfect phylogenetic forest problem. In COCOON07, Vol. 4598:16-26 of LNCS, springer, 2007.
Keywords: perfect, phylogenetic network, phylogeny.
Note: http://dx.doi.org/10.1007/978-3-540-73545-8_5.

@InProceedings{WuGusfield2007c,
AUTHOR = {Wu, Yufeng and Gusfield, Dan},
TITLE = {A new recombination lower bound and the minimum perfect phylogenetic forest problem},
YEAR = {2007},
BOOKTITLE = {COCOON07},
VOLUME = {4598},
PAGES = {16-26},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-540-73545-8_5},
NOTE = {http://dx.doi.org/10.1007/978-3-540-73545-8_5},
ANNOTE = {CITE : },
KEYWORDS = {perfect, phylogenetic network, phylogeny}
}

24

Yuanyi Zhang, Lichen Bao and Sergey Bereg. Optimizing Split Networks. 2007.
Note: UC Dallas Computer Science Technical Report UTDCS-08-07.

@Misc{ZBB2007,
AUTHOR = {Zhang, Yuanyi and Bao, Lichen and Bereg, Sergey},
TITLE = {Optimizing Split Networks},
YEAR = {2007},
NOTE = {UC Dallas Computer Science Technical Report UTDCS-08-07},
ANNOTE = {CITE : }
}

25

David Bryant, Vincent Moulton and Andreas Spillner. Consistency of the Neighbor-Net Algorithm. In AMB, Vol. 2(8), 2007.
Keywords: abstract network, consistency, from distances, NeighborNet.
Note: http://dx.doi.org/10.1186/1748-7188-2-8.

Toggle abstract

@Article{BMS2007,
AUTHOR = {Bryant, David and Moulton, Vincent and Spillner, Andreas},
TITLE = {Consistency of the Neighbor-Net Algorithm},
YEAR = {2007},
JOURNAL = {AMB},
VOLUME = {2},
NUMBER = {8},
URL = {http://dx.doi.org/10.1186/1748-7188-2-8},
NOTE = {http://dx.doi.org/10.1186/1748-7188-2-8},
ANNOTE = {BIBUPDATE : 20071117},
KEYWORDS = {abstract network, consistency, from distances, NeighborNet}
}

26

Maria S. Poptsova and J. Peter Gogarten. The power of phylogenetic approaches to detect horizontally transferred genes. In BMCEB, Vol. 7(45), 2007.
Keywords: evaluation, from rooted trees, lateral gene transfer, Program EEEP.
Note: http://dx.doi.org/10.1186/1471-2148-7-45.

Toggle abstract

@Article{PoptsovaGogarten2007,
AUTHOR = {Poptsova, Maria S. and Gogarten, J. Peter},
TITLE = {The power of phylogenetic approaches to detect horizontally transferred genes},
YEAR = {2007},
JOURNAL = {BMCEB},
VOLUME = {7},
NUMBER = {45},
URL = {http://dx.doi.org/10.1186/1471-2148-7-45},
NOTE = {http://dx.doi.org/10.1186/1471-2148-7-45},
ANNOTE = {BIBUPDATE : 20071120},
KEYWORDS = {evaluation, from rooted trees, lateral gene transfer, Program EEEP}
}

27

Daniel H. Huson, Daniel C. Richter, Christian Rausch, Tobias Dezulian, Markus Franz and Regula Rupp. Dendroscope: An interactive viewer for large phylogenetic trees. In BMCB, Vol. 8:460, 2007.
Keywords: phylogeny, Program Dendroscope, software, visualization.
Note: http://dx.doi.org/10.1186/1471-2105-8-460, slides available at http://www.newton.cam.ac.uk/webseminars/pg+ws/2007/plg/plgw01/0903/huson/, software freely available from http://www.dendroscope.org.

Toggle abstract

@Article{HDFRRR2007,
AUTHOR = {Huson, Daniel H. and Richter, Daniel C. and Rausch, Christian and Dezulian, Tobias and Franz, Markus and Rupp, Regula},
TITLE = {Dendroscope: An interactive viewer for large phylogenetic trees},
YEAR = {2007},
JOURNAL = {BMCB},
VOLUME = {8},
PAGES = {460},
URL = {http://dx.doi.org/10.1186/1471-2105-8-460},
NOTE = {http://dx.doi.org/10.1186/1471-2105-8-460, slides available at http://www.newton.cam.ac.uk/webseminars/pg+ws/2007/plg/plgw01/0903/huson/, software freely available from http://www.dendroscope.org},
ANNOTE = {CITE : },
KEYWORDS = {phylogeny, Program Dendroscope, software, visualization}
}

28

Monique M. Morin. Phylogenetic Networks: Simulation, Characterization, and Reconstruction. PhD thesis, The University of New Mexico, U.S.A., 2007.
Keywords: evaluation, explicit network, hybridization, lateral gene transfer, phylogenetic network, phylogeny, Program NetGen, simulation, software.
Note: http://www.cs.unm.edu/~morin/morin_phd.pdf.

@PhdThesis{Morin2007,
AUTHOR = {Morin, Monique M.},
TITLE = {Phylogenetic Networks: Simulation, Characterization, and Reconstruction},
YEAR = {2007},
SCHOOL = {The University of New Mexico, U.S.A.},
NOTE = {http://www.cs.unm.edu/~morin/morin_phd.pdf},
ANNOTE = {CITE : },
KEYWORDS = {evaluation, explicit network, hybridization, lateral gene transfer, phylogenetic network, phylogeny, Program NetGen, simulation, software}
}

29

Dan Gusfield, Vikas Bansal, Vineet Bafna and Yun S. Song. A Decomposition Theory for Phylogenetic Networks and Incompatible Characters. In JCB, Vol. 14(10):1247-1272, 2007.
Keywords: explicit network, from sequences, galled tree, phylogenetic network, phylogeny, Program Beagle, Program GalledTree, recombination, reconstruction, software.
Note: http://www.eecs.berkeley.edu/~yss/Pub/decomposition.pdf.

@Article{GBBS2007,
AUTHOR = {Gusfield, Dan and Bansal, Vikas and Bafna, Vineet and Song, Yun S.},
TITLE = {A Decomposition Theory for Phylogenetic Networks and Incompatible Characters},
YEAR = {2007},
JOURNAL = {JCB},
VOLUME = {14},
NUMBER = {10},
PAGES = {1247-1272},
URL = {http://dx.doi.org/10.1089/cmb.2006.0137},
NOTE = {http://www.eecs.berkeley.edu/~yss/Pub/decomposition.pdf},
ANNOTE = {BIBUPDATE : 20071206},
KEYWORDS = {explicit network, from sequences, galled tree, phylogenetic network, phylogeny, Program Beagle, Program GalledTree, recombination, reconstruction, software}
}

30

Tamir Tuller and Sagi Snir. The NET-HMM: a HMM Based Likelihood Model for Evolutionary Networks. 2007.
Keywords: lateral gene transfer, likelihood, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: Poster presented at the eleventh Annual International Conference on Research in Computational Molecular Biology (RECOMB'07), http://www.qb3.org/recomb07/posters/Tuller013043013RECOMB_HMM1.pdf.

@Misc{TullerSnir2007,
AUTHOR = {Tuller, Tamir and Snir, Sagi},
TITLE = {The NET-HMM: a HMM Based Likelihood Model for Evolutionary Networks},
YEAR = {2007},
NOTE = {Poster presented at the eleventh Annual International Conference on Research in Computational Molecular Biology (RECOMB'07), http://www.qb3.org/recomb07/posters/Tuller013043013RECOMB_HMM1.pdf},
ANNOTE = {CITE : },
KEYWORDS = {lateral gene transfer, likelihood, phylogenetic network, phylogeny, reconstruction, statistical model}
}

31

Yun S. Song, Zhihong Ding, Dan Gusfield, Charles Langley and Yufeng Wu. Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations. In JCB, Vol. 14(10):1273-1286, 2007.
Keywords: ARG, from sequences, phylogenetic network, phylogeny, Program SHRUB, reconstruction.
Note: http://dx.doi.org/10.1089/cmb.2007.0096.

Toggle abstract

@Article{SDGLW2007,
AUTHOR = {Song, Yun S. and Ding, Zhihong and Gusfield, Dan and Langley, Charles and Wu, Yufeng},
TITLE = {Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations},
YEAR = {2007},
JOURNAL = {JCB},
VOLUME = {14},
NUMBER = {10},
PAGES = {1273-1286},
URL = {http://dx.doi.org/10.1089/cmb.2007.0096},
NOTE = {http://dx.doi.org/10.1089/cmb.2007.0096},
ANNOTE = {BIBUPDATE : 20071212},
KEYWORDS = {ARG, from sequences, phylogenetic network, phylogeny, Program SHRUB, reconstruction}
}

32

Andreas W. M. Dress, Katharina Huber, Jacobus Koolen and Vincent Moulton. An Algorithm for Computing Virtual Cut Points in Finite Metric Spaces. In COCOA07, Vol. 4616:4-10 of LNCS, springer, 2007.
Keywords: from distances.
Note: http://dx.doi.org/10.1007/978-3-540-73556-4_3.

@InProceedings{DHKM2007,
AUTHOR = {Dress, Andreas W. M. and Huber, Katharina and Koolen, Jacobus and Moulton, Vincent},
TITLE = {An Algorithm for Computing Virtual Cut Points in Finite Metric Spaces},
YEAR = {2007},
BOOKTITLE = {COCOA07},
VOLUME = {4616},
PAGES = {4-10},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-540-73556-4_3},
NOTE = {http://dx.doi.org/10.1007/978-3-540-73556-4_3},
ANNOTE = {BIBUPDATE : 20071218},
KEYWORDS = {from distances}
}

33

Patricia Buendia and Giri Narasimhan. Searching for Recombinant Donors in a Phylogenetic Network of Serial Samples. In ISBRA07, Vol. 4463:109-120 of LNCS, springer, 2007.
Keywords: evaluation, phylogenetic network, phylogeny, recombination, recombination detection.
Note: http://dx.doi.org/10.1007/978-3-540-72031-7_10.

@InProceedings{BuendiaNarasimhan2007,
AUTHOR = {Buendia, Patricia and Narasimhan, Giri},
TITLE = {Searching for Recombinant Donors in a Phylogenetic Network of Serial Samples},
YEAR = {2007},
BOOKTITLE = {ISBRA07},
VOLUME = {4463},
PAGES = {109-120},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-540-72031-7_10},
NOTE = {http://dx.doi.org/10.1007/978-3-540-72031-7_10},
ANNOTE = {CITE : },
KEYWORDS = {evaluation, phylogenetic network, phylogeny, recombination, recombination detection}
}

34

Patricia Buendia and Giri Narasimhan. Sliding MinPD: Building evolutionary networks of serial samples via an automated recombination detection approach. In BIO, Vol. 23(22):2993-3000, 2007.
Keywords: from sequences, phylogenetic network, phylogeny, Program Sliding MinPD, recombination, recombination detection, serial evolutionary networks, software.
Note: http://dx.doi.org/10.1093/bioinformatics/btm413.

Toggle abstract

@Article{BuendiaNarasimhan2007b,
AUTHOR = {Buendia, Patricia and Narasimhan, Giri},
TITLE = {Sliding MinPD: Building evolutionary networks of serial samples via an automated recombination detection approach},
YEAR = {2007},
JOURNAL = {BIO},
VOLUME = {23},
NUMBER = {22},
PAGES = {2993-3000},
URL = {http://dx.doi.org/10.1093/bioinformatics/btm413},
NOTE = {http://dx.doi.org/10.1093/bioinformatics/btm413},
ANNOTE = {BIBUPDATE : 20071228},
KEYWORDS = {from sequences, phylogenetic network, phylogeny, Program Sliding MinPD, recombination, recombination detection, serial evolutionary networks, software}
}

35

Alice Lesser. Optimal and Hereditarily Optimal Realizations of Metric Spaces. PhD thesis, Uppsala University, Sweden, 2007.
Keywords: from distances, optimal realization, phylogenetic network, phylogeny, realization.
Note: http://www.diva-portal.org/diva/getDocument?urn_nbn_se_uu_diva-8297-2__fulltext.pdf.

@PhdThesis{Lesser2007,
AUTHOR = {Lesser, Alice},
TITLE = {Optimal and Hereditarily Optimal Realizations of Metric Spaces},
YEAR = {2007},
SCHOOL = {Uppsala University, Sweden},
NOTE = {http://www.diva-portal.org/diva/getDocument?urn_nbn_se_uu_diva-8297-2__fulltext.pdf},
ANNOTE = {CITE : },
KEYWORDS = {from distances, optimal realization, phylogenetic network, phylogeny, realization}
}

36

Bastienne Vriesendorp. Phylogenenetworks, exploring reticulate evolution and its consequences for phylogenetic reconstruction. PhD thesis, Wageningen University, The Netherlands, 2007.
Keywords: consensus, distance between networks, evaluation, hybridization, median network, NeighborNet, parsimony, phylogenetic network, phylogeny, Program SplitsTree, split decomposition, survey.
Note: http://library.wur.nl/wda/dissertations/dis4239.pdf.

@PhdThesis{Vriesendorp2007,
AUTHOR = {Vriesendorp, Bastienne},
TITLE = {Phylogenenetworks, exploring reticulate evolution and its consequences for phylogenetic reconstruction},
YEAR = {2007},
SCHOOL = {Wageningen University, The Netherlands},
NOTE = {http://library.wur.nl/wda/dissertations/dis4239.pdf},
ANNOTE = {CITE : },
KEYWORDS = {consensus, distance between networks, evaluation, hybridization, median network, NeighborNet, parsimony, phylogenetic network, phylogeny, Program SplitsTree, split decomposition, survey}
}

37

David Penny, Barbara R. Holland and Mike Hendy. Phylogenetics: Parsimony, Networks and Distance Methods. In D. Balding, M. Bishop and C. Cannings editors, Handbook of Statistical Genetics, 3rd Ed, Pages 489-532, John Wiley and Sons Ltd, 2007.
Keywords: survey.
Note: http://www.amazon.fr/gp/reader/0470058307/ref=sib_dp_pt#reader-link.

@InBook{PHH2007,
AUTHOR = {Penny, David and Holland, Barbara R. and Hendy, Mike},
TITLE = {Phylogenetics: Parsimony, Networks and Distance Methods},
YEAR = {2007},
BOOKTITLE = {Handbook of Statistical Genetics, 3rd Ed},
PAGES = {489-532},
EDITOR = {Balding, D. and Bishop, M. and Cannings, C.},
PUBLISHER = {John Wiley and Sons Ltd},
URL = {http://dx.doi.org/10.1002/9780470061619.ch16},
NOTE = {http://www.amazon.fr/gp/reader/0470058307/ref=sib_dp_pt#reader-link},
ANNOTE = {CITE : },
KEYWORDS = {survey}
}

38

D. S. Rao, G. N. Kumar, Dheeresh K. Mallick and Prasanta K. Jana. Parallel Construction of Conflict Graph for Phylogenetic Network Problem. In Pattern Recognition and Machine Intelligence (PReMI'07), Vol. 4815:398-405 of LNCS, springer, 2007.
Note: http://dx.doi.org/10.1007/978-3-540-77046-6_49.

@InProceedings{RKMJ2007,
AUTHOR = {Rao, D. S. and Kumar, G. N. and Mallick, Dheeresh K. and Jana, Prasanta K.},
TITLE = {Parallel Construction of Conflict Graph for Phylogenetic Network Problem},
YEAR = {2007},
BOOKTITLE = {Pattern Recognition and Machine Intelligence (PReMI'07)},
VOLUME = {4815},
PAGES = {398-405},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-540-77046-6_49},
NOTE = {http://dx.doi.org/10.1007/978-3-540-77046-6_49},
ANNOTE = {BIBUPDATE : 20080513}
}

39

Joanna L. Davies, Frantisek Simancík, Rune Lyngsø, Thomas Mailund and Jotun Hein. On Recombination-Induced Multiple and Simultaneous Coalescent Events. In GEN, Vol. 177:2151-2160, 2007.
Keywords: coalescent, phylogenetic network, phylogeny, recombination, statistical model.
Note: http://dx.doi.org/10.1534/genetics.107.071126.

Toggle abstract

@Article{DSLMH2007,
AUTHOR = {Davies, Joanna L. and Simanc{\~A}�k, Frantisek and Lyngs{\~A}�, Rune and Mailund, Thomas and Hein, Jotun},
TITLE = {On Recombination-Induced Multiple and Simultaneous Coalescent Events},
YEAR = {2007},
JOURNAL = {GEN},
VOLUME = {177},
PAGES = {2151-2160},
URL = {http://dx.doi.org/10.1534/genetics.107.071126},
NOTE = {http://dx.doi.org/10.1534/genetics.107.071126},
ANNOTE = {CITE : },
KEYWORDS = {coalescent, phylogenetic network, phylogeny, recombination, statistical model}
}

40

Galina Glazko, Vladimir Makarenkov, Jing Liu and Arcady Mushegian. Evolutionary history of bacteriophages with double-stranded DNA genomes. In Biology Direct, Vol. 2(36), 2007.
Keywords: explicit network, from sequences, phylogenetic network, phylogeny, Program T REX.
Note: http://dx.doi.org/10.1186/1745-6150-2-36.

Toggle abstract

@Article{GMLM2007,
AUTHOR = {Glazko, Galina and Makarenkov, Vladimir and Liu, Jing and Mushegian, Arcady},
TITLE = {Evolutionary history of bacteriophages with double-stranded DNA genomes},
YEAR = {2007},
JOURNAL = {Biology Direct},
VOLUME = {2},
NUMBER = {36},
URL = {http://dx.doi.org/10.1186/1745-6150-2-36},
NOTE = {http://dx.doi.org/10.1186/1745-6150-2-36},
ANNOTE = {BIBUPDATE : 20081110},
KEYWORDS = {explicit network, from sequences, phylogenetic network, phylogeny, Program T REX}
}

41

Cuong Than, Derek Ruths, Hideki Innan and Luay Nakhleh. Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions. In JCB, Vol. 14(4):517-535, 2007.
Keywords: counting, explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, Program LatTrans, Program PhyloNet.
Note: http://www.cs.rice.edu/~nakhleh/Papers/recombcg06-jcb.pdf.

@Article{TRIN2007,
AUTHOR = {Than, Cuong and Ruths, Derek and Innan, Hideki and Nakhleh, Luay},
TITLE = {Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions},
YEAR = {2007},
JOURNAL = {JCB},
VOLUME = {14},
NUMBER = {4},
PAGES = {517-535},
URL = {http://dx.doi.org/10.1089/cmb.2007.A010},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/recombcg06-jcb.pdf},
ANNOTE = {BIBUPDATE : 20081127},
KEYWORDS = {counting, explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, Program LatTrans, Program PhyloNet}
}

42

Hans-Jürgen Bandelt and Arne Dür. Translating DNA data tables into quasi-median networks for parsimony analysis and error detection. In MPE, Vol. 42(1):256-271, 2007.
Keywords: abstract network, from sequences, parsimony, phylogenetic network, phylogeny, quasi-median network, reconstruction.
Note: http://dx.doi.org/10.1016/j.ympev.2006.07.013.

Toggle abstract

@Article{BandeltDurr2007,
AUTHOR = {Bandelt, Hans-J{\~A}�rgen and D{\~A}�r, Arne},
TITLE = {Translating DNA data tables into quasi-median networks for parsimony analysis and error detection},
YEAR = {2007},
JOURNAL = {MPE},
VOLUME = {42},
NUMBER = {1},
PAGES = {256-271},
URL = {http://dx.doi.org/10.1016/j.ympev.2006.07.013},
NOTE = {http://dx.doi.org/10.1016/j.ympev.2006.07.013},
KEYWORDS = {abstract network, from sequences, parsimony, phylogenetic network, phylogeny, quasi-median network, reconstruction}
}

43

Nicolas Galtier. A model of horizontal gene transfer and the bacterial phylogeny problem. In Systematic Biology, Vol. 56(4):633-642, 2007.
Keywords: explicit network, generation, lateral gene transfer, phylogenetic network, phylogeny, Program HGT_simul, software, statistical model.
Note: http://dx.doi.org/10.1080/10635150701546231.

Toggle abstract

@Article{Galtier2007,
AUTHOR = {Galtier, Nicolas},
TITLE = {A model of horizontal gene transfer and the bacterial phylogeny problem},
YEAR = {2007},
JOURNAL = {Systematic Biology},
VOLUME = {56},
NUMBER = {4},
PAGES = {633-642},
URL = {http://dx.doi.org/10.1080/10635150701546231},
NOTE = {http://dx.doi.org/10.1080/10635150701546231},
KEYWORDS = {explicit network, generation, lateral gene transfer, phylogenetic network, phylogeny, Program HGT_simul, software, statistical model}
}

44

Yuanyi Zhang. Optimization Algorithms for Phylogenetic Networks. PhD thesis, University of Texas at Dallas, U.S.A., 2007.
Keywords: abstract network, explicit network, from distances, phylogenetic network, phylogeny, reconstruction, split, split network, visualization.
Note: http://proquest.umi.com/pqdlink?did=1421626541&sid=1&Fmt=6&clientId=176295&RQT=309&VName=PQD.

@PhdThesis{Zhang2007,
AUTHOR = {Zhang, Yuanyi},
TITLE = {Optimization Algorithms for Phylogenetic Networks},
YEAR = {2007},
SCHOOL = {University of Texas at Dallas, U.S.A.},
NOTE = {http://proquest.umi.com/pqdlink?did=1421626541{\&}sid=1{\&}Fmt=6{\&}clientId=176295{\&}RQT=309{\&}VName=PQD},
KEYWORDS = {abstract network, explicit network, from distances, phylogenetic network, phylogeny, reconstruction, split, split network, visualization}
}

45

Hadas Birin, Zohar Gal-Or, Isaac Elias and Tamir Tuller. Inferring Models of Rearrangements, Recombinations, and Horizontal Transfers by the Minimum Evolution Criterion. In WABI07, Vol. 4645:111-123 of LNCS, springer, 2007.
Keywords: explicit network, from sequences, phylogenetic network, phylogeny, reconstruction.
Note: http://safrabio.cs.tau.ac.il/download/Papers/Birin_et_al.pdf.

@InProceedings{BGET2007,
AUTHOR = {Birin, Hadas and Gal-Or, Zohar and Elias, Isaac and Tuller, Tamir},
TITLE = {Inferring Models of Rearrangements, Recombinations, and Horizontal Transfers by the Minimum Evolution Criterion},
YEAR = {2007},
BOOKTITLE = {WABI07},
VOLUME = {4645},
PAGES = {111-123},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-540-74126-8_11},
NOTE = {http://safrabio.cs.tau.ac.il/download/Papers/Birin_et_al.pdf},
KEYWORDS = {explicit network, from sequences, phylogenetic network, phylogeny, reconstruction}
}

46

Ethan Cecchetti. Orientability of Phylogenetic Network Graphs. In Rose Hulman Undergraduate Math Journal, Vol. 8(2), 2007.
Keywords: characterization, explicit network, phylogenetic network.
Note: http://www.rose-hulman.edu/mathjournal/v8n2.php.

@Article{Cecchetti2007,
AUTHOR = {Cecchetti, Ethan},
TITLE = {Orientability of Phylogenetic Network Graphs},
YEAR = {2007},
JOURNAL = {Rose Hulman Undergraduate Math Journal},
VOLUME = {8},
NUMBER = {2},
NOTE = {http://www.rose-hulman.edu/mathjournal/v8n2.php},
KEYWORDS = {characterization, explicit network, phylogenetic network}
}

2006

1

Sergey Bereg and Yuanyi Zhang. Phylogenetic Networks Based on the Molecular Clock Hypothesis. In TCBB, Vol. 3(4), 2006.
Note: http://www.utdallas.edu/~yzhang/Homepage/Papers/prep-tcbb.pdf.

Toggle abstract

@Article{BeregZhang2006,
AUTHOR = {Bereg, Sergey and Zhang, Yuanyi},
TITLE = {Phylogenetic Networks Based on the Molecular Clock Hypothesis},
YEAR = {2006},
JOURNAL = {TCBB},
VOLUME = {3},
NUMBER = {4},
URL = {http://dx.doi.org/10.1109/tcbb.2007.1043},
NOTE = {http://www.utdallas.edu/~yzhang/Homepage/Papers/prep-tcbb.pdf},
ANNOTE = {CITE : }
}

2

Mihaela Baroni, Charles Semple and Mike Steel. Hybrids in Real Time. In Systematic Biology, Vol. 55(1):46-56, 2006.
Keywords: agreement forest, from rooted trees, phylogenetic network, phylogeny, polynomial, reconstruction, time consistent network.
Note: http://www.math.canterbury.ac.nz/~m.steel/Non_UC/files/research/hybrids.pdf.

Toggle abstract

@Article{BSS2006,
AUTHOR = {Baroni, Mihaela and Semple, Charles and Steel, Mike},
TITLE = {Hybrids in Real Time},
YEAR = {2006},
JOURNAL = {Systematic Biology},
VOLUME = {55},
NUMBER = {1},
PAGES = {46-56},
URL = {http://dx.doi.org/10.1080/10635150500431197},
NOTE = {http://www.math.canterbury.ac.nz/~m.steel/Non_UC/files/research/hybrids.pdf},
ANNOTE = {CITE : },
KEYWORDS = {agreement forest, from rooted trees, phylogenetic network, phylogeny, polynomial, reconstruction, time consistent network}
}

3

Ho-Leung Chan, Jesper Jansson, Tak-Wah Lam and Siu-Ming Yiu. Reconstructing an Ultrametric Galled Phylogenetic Network from a Distance Matrix. In JBCB, Vol. 4(4):807-832, 2006.
Keywords: explicit network, from distances, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.df.lth.se/~jj/Publications/dist_ugn7_JBCB2006.pdf.

Toggle abstract

@Article{CJLY2006,
AUTHOR = {Chan, Ho-Leung and Jansson, Jesper and Lam, Tak-Wah and Yiu, Siu-Ming},
TITLE = {Reconstructing an Ultrametric Galled Phylogenetic Network from a Distance Matrix},
YEAR = {2006},
JOURNAL = {JBCB},
VOLUME = {4},
NUMBER = {4},
PAGES = {807-832},
URL = {http://dx.doi.org/10.1142/S0219720006002211},
NOTE = {http://www.df.lth.se/~jj/Publications/dist_ugn7_JBCB2006.pdf},
ANNOTE = {CITE : },
KEYWORDS = {explicit network, from distances, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction}
}

4

Ying-Jun He, Trinh N. D. Huynh, Jesper Jansson and Wing-Kin Sung. Inferring Phylogenetic Relationships Avoiding Forbidden Rooted Triplets. In JBCB, Vol. 4(1):59-74, 2006.
Note: http://www.df.lth.se/~jj/Publications/forb_triplets7_JBCB2006.pdf.

Toggle abstract

@Article{HHJS2006,
AUTHOR = {He, Ying-Jun and Huynh, Trinh N. D. and Jansson, Jesper and Sung, Wing-Kin},
TITLE = {Inferring Phylogenetic Relationships Avoiding Forbidden Rooted Triplets},
YEAR = {2006},
JOURNAL = {JBCB},
VOLUME = {4},
NUMBER = {1},
PAGES = {59-74},
URL = {http://dx.doi.org/10.1142/S0219720006001709},
NOTE = {http://www.df.lth.se/~jj/Publications/forb_triplets7_JBCB2006.pdf},
ANNOTE = {CITE : }
}

5

Barbara R. Holland, Lars S. Jermiin and Vincent Moulton. Improved Consensus Network Techniques for Genome-Scale Phylogeny. In Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005 (SMBE'05), Vol. 23(5):848-855 of MBE, 2006.
Keywords: consensus.
Note: http://dx.doi.org/10.1093/molbev/msj061.

@InProceedings{HJM2006,
AUTHOR = {Holland, Barbara R. and Jermiin, Lars S. and Moulton, Vincent},
TITLE = {Improved Consensus Network Techniques for Genome-Scale Phylogeny},
YEAR = {2006},
BOOKTITLE = {Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005 (SMBE'05)},
VOLUME = {23(5)},
PAGES = {848-855},
SERIES = {MBE},
URL = {http://dx.doi.org/10.1093/molbev/msj061},
NOTE = {http://dx.doi.org/10.1093/molbev/msj061},
ANNOTE = {BIBUPDATE : 20070920},
KEYWORDS = {consensus}
}

6

Daniel H. Huson, Mike Steel and James B. Whitfield. Reducing Distortion in Phylogenetic Networks. In WABI06, Vol. 4175:150-161 of LNCS, springer, 2006.
Keywords: phylogenetic network, reconstruction.
Note: http://www.math.canterbury.ac.nz/~m.steel/research/Non_UC/files/distortion.pdf.

@InProceedings{HSW2006,
AUTHOR = {Huson, Daniel H. and Steel, Mike and Whitfield, James B.},
TITLE = {Reducing Distortion in Phylogenetic Networks},
YEAR = {2006},
BOOKTITLE = {WABI06},
VOLUME = {4175},
PAGES = {150-161},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/11851561_14},
NOTE = {http://www.math.canterbury.ac.nz/~m.steel/research/Non_UC/files/distortion.pdf},
ANNOTE = {CITE : },
KEYWORDS = {phylogenetic network, reconstruction}
}

7

Vincent Moulton and Katharina Huber. Phylogenetic networks from multi-labelled trees. In JOMB, Vol. 52(5):613-632, 2006.
Keywords: duplication, explicit network, from multilabeled tree, phylogenetic network, phylogeny, Program PADRE, reconstruction.
Note: http://www.uea.ac.uk/~a043878/jmb.pdf.

Toggle abstract

@Article{HuberMoulton2006,
AUTHOR = {Moulton, Vincent and Huber, Katharina},
TITLE = {Phylogenetic networks from multi-labelled trees},
YEAR = {2006},
JOURNAL = {JOMB},
VOLUME = {52},
NUMBER = {5},
PAGES = {613-632},
URL = {http://dx.doi.org/10.1007/s00285-005-0365-z},
NOTE = {http://www.uea.ac.uk/~a043878/jmb.pdf},
ANNOTE = {BIBUPDATE : 20070924},
KEYWORDS = {duplication, explicit network, from multilabeled tree, phylogenetic network, phylogeny, Program PADRE, reconstruction}
}

8

Daniel H. Huson and David Bryant. Application of Phylogenetic Networks in Evolutionary Studies. In MBE, Vol. 23(2):254-267, 2006.
Keywords: abstract network, phylogenetic network, phylogeny, Program SplitsTree, software, survey.
Note: http://dx.doi.org/10.1093/molbev/msj030, software available from www.splitstree.org.

Toggle abstract

@Article{HusonBryant2006,
AUTHOR = {Huson, Daniel H. and Bryant, David},
TITLE = {Application of Phylogenetic Networks in Evolutionary Studies},
YEAR = {2006},
JOURNAL = {MBE},
VOLUME = {23},
NUMBER = {2},
PAGES = {254-267},
URL = {http://dx.doi.org/10.1093/molbev/msj030},
NOTE = {http://dx.doi.org/10.1093/molbev/msj030, software available from www.splitstree.org},
ANNOTE = {http://dx.doi.org/10.1093/molbev/msj030},
KEYWORDS = {abstract network, phylogenetic network, phylogeny, Program SplitsTree, software, survey}
}

9

Jesper Jansson and Wing-Kin Sung. Inferring a level-1 phylogenetic network from a dense set of rooted triplets. In TCS, Vol. 363(1):60-68, 2006.
Keywords: explicit network, from triplets, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.df.lth.se/~jj/Publications/ipnrt8_TCS2006.pdf.

Toggle abstract

@Article{JanssonSung2006,
AUTHOR = {Jansson, Jesper and Sung, Wing-Kin},
TITLE = {Inferring a level-1 phylogenetic network from a dense set of rooted triplets},
YEAR = {2006},
JOURNAL = {TCS},
VOLUME = {363},
NUMBER = {1},
PAGES = {60-68},
URL = {http://dx.doi.org/10.1016/j.tcs.2006.06.022},
NOTE = {http://www.df.lth.se/~jj/Publications/ipnrt8_TCS2006.pdf},
KEYWORDS = {explicit network, from triplets, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, polynomial, reconstruction}
}

10

Jesper Jansson, Nguyen Bao Nguyen and Wing-Kin Sung. Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network. In SICOMP, Vol. 35(5):1098-1121, 2006.
Keywords: approximation, explicit network, from triplets, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.df.lth.se/~jj/Publications/triplets_to_gn7_SICOMP2006.pdf.

Toggle abstract

@Article{JNS2006,
AUTHOR = {Jansson, Jesper and Nguyen, Nguyen Bao and Sung, Wing-Kin},
TITLE = {Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network},
YEAR = {2006},
JOURNAL = {SICOMP},
VOLUME = {35},
NUMBER = {5},
PAGES = {1098-1121},
URL = {http://dx.doi.org/10.1137/S0097539704446529},
NOTE = {http://www.df.lth.se/~jj/Publications/triplets_to_gn7_SICOMP2006.pdf},
KEYWORDS = {approximation, explicit network, from triplets, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction}
}

11

Guohua Jin, Luay Nakhleh, Sagi Snir and Tamir Tuller. Maximum Likelihood of Phylogenetic Networks. In BIO, Vol. 22(21):2604-2611, 2006.
Keywords: explicit network, likelihood, phylogenetic network, phylogeny, Program Nepal, reconstruction.
Note: http://www.cs.rice.edu/~nakhleh/Papers/NetworksML06.pdf, supplementary material: http://www.cs.rice.edu/~nakhleh/Papers/Supp-ML.pdf.

@Article{JNST2006b,
AUTHOR = {Jin, Guohua and Nakhleh, Luay and Snir, Sagi and Tuller, Tamir},
TITLE = {Maximum Likelihood of Phylogenetic Networks},
YEAR = {2006},
JOURNAL = {BIO},
VOLUME = {22},
NUMBER = {21},
PAGES = {2604-2611},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl452},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/NetworksML06.pdf, supplementary material: http://www.cs.rice.edu/~nakhleh/Papers/Supp-ML.pdf},
ANNOTE = {BIBUPDATE : 20070917},
KEYWORDS = {explicit network, likelihood, phylogenetic network, phylogeny, Program Nepal, reconstruction}
}

12

Iyad A. Kanj, Luay Nakhleh and Ge Xia. Reconstructing Evolution of Natural Languages: Complexity and Parameterized Algorithms. In COCOON06, Vol. 4112:299-308 of LNCS, springer, 2006.
Note: http://www.cs.rice.edu/~nakhleh/Papers/cocoon06.pdf.

@InProceedings{KNX2006,
AUTHOR = {Kanj, Iyad A. and Nakhleh, Luay and Xia, Ge},
TITLE = {Reconstructing Evolution of Natural Languages: Complexity and Parameterized Algorithms},
YEAR = {2006},
BOOKTITLE = {COCOON06},
VOLUME = {4112},
PAGES = {299-308},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/11809678_32},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/cocoon06.pdf},
ANNOTE = {BIBUPDATE : 20070917}
}

13

Vladimir Makarenkov, Dmytro Kevorkov and Pierre Legendre. Phylogenetic Network Construction Approaches. In Applied Mycology and Biotechnology, Vol. 6:61-97, 2006.
Keywords: from distances, hybridization, lateral gene transfer, median network, NeighborNet, netting, Program Arlequin, Program Network, Program Pyramids, Program Reticlad, Program SplitsTree, Program T REX, Program TCS, Program WeakHierarchies, pyramid, reticulogram, split, split decomposition, split network, survey, weak hierarchy.
Note: http://www.labunix.uqam.ca/~makarenv/makarenv/MKL_article.pdf.

@InBook{MKL2006,
AUTHOR = {Makarenkov, Vladimir and Kevorkov, Dmytro and Legendre, Pierre},
TITLE = {Phylogenetic Network Construction Approaches},
YEAR = {2006},
BOOKTITLE = {Applied Mycology and Biotechnology},
VOLUME = {6},
PAGES = {61-97},
URL = {http://dx.doi.org/10.1016/s1874-5334(06)80006-7},
NOTE = {http://www.labunix.uqam.ca/~makarenv/makarenv/MKL_article.pdf},
ANNOTE = {BIBUPDATE : 20070918},
KEYWORDS = {from distances, hybridization, lateral gene transfer, median network, NeighborNet, netting, Program Arlequin, Program Network, Program Pyramids, Program Reticlad, Program SplitsTree, Program T REX, Program TCS, Program WeakHierarchies, pyramid, reticulogram, split, split decomposition, split network, survey, weak hierarchy}
}

14

Monique M. Morin and Bernard M. E. Moret. NetGen: generating phylogenetic networks with diploid hybrids. In BIO, Vol. 22(15):1921-1923, 2006.
Keywords: generation, hybridization, Program NetGen, software.
Note: http://dx.doi.org/10.1093/bioinformatics/btl191.

Toggle abstract

@Article{MorinMoret2006,
AUTHOR = {Morin, Monique M. and Moret, Bernard M. E.},
TITLE = {NetGen: generating phylogenetic networks with diploid hybrids},
YEAR = {2006},
JOURNAL = {BIO},
VOLUME = {22},
NUMBER = {15},
PAGES = {1921-1923},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl191},
NOTE = {http://dx.doi.org/10.1093/bioinformatics/btl191},
ANNOTE = {BIBUPDATE : 20070918},
KEYWORDS = {generation, hybridization, Program NetGen, software}
}

15

Charles Semple and Mike Steel. Unicyclic networks: compatibility and enumeration. In TCBB, Vol. 3(1):84-91, 2006.
Keywords: counting, explicit network, galled tree, unicyclic network.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/SS06.pdf.

@Article{SempleSteel2006,
AUTHOR = {Semple, Charles and Steel, Mike},
TITLE = {Unicyclic networks: compatibility and enumeration},
YEAR = {2006},
JOURNAL = {TCBB},
VOLUME = {3},
NUMBER = {1},
PAGES = {84-91},
URL = {http://dx.doi.org/10.1109/tcbb.2006.14},
NOTE = {http://www.math.canterbury.ac.nz/~c.semple/papers/SS06.pdf},
ANNOTE = {ISSUE : 1},
KEYWORDS = {counting, explicit network, galled tree, unicyclic network}
}

16

Cuong Than, Derek Ruths, Hideki Innan and Luay Nakhleh. Identifiability Issues in Phylogeny-Based Detection of Horizontal Gene Transfer. In Proceedings of the Fourth RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG'06), Vol. 4205:215-229 of LNCS, springer, 2006.
Keywords: explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, Program LatTrans, Program PhyloNet.
Note: http://www.cs.rice.edu/~nakhleh/Papers/recombcg06-final.pdf.

@InProceedings{TRIN2006,
AUTHOR = {Than, Cuong and Ruths, Derek and Innan, Hideki and Nakhleh, Luay},
TITLE = {Identifiability Issues in Phylogeny-Based Detection of Horizontal Gene Transfer},
YEAR = {2006},
BOOKTITLE = {Proceedings of the Fourth RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG'06)},
VOLUME = {4205},
PAGES = {215-229},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/11864127_17},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/recombcg06-final.pdf},
ANNOTE = {BIBUPDATE : 20070917},
KEYWORDS = {explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, Program LatTrans, Program PhyloNet}
}

17

Stephen J. Willson. Unique solvability of certain hybrid networks from their distances. In ACOM, Vol. 10(1):165-178, 2006.
Keywords: from distances, from network, labeling, phylogenetic network, phylogeny.
Note: http://www.public.iastate.edu/~swillson/Solvability.pdf.

@Article{Willson2006a,
AUTHOR = {Willson, Stephen J.},
TITLE = {Unique solvability of certain hybrid networks from their distances},
YEAR = {2006},
JOURNAL = {ACOM},
VOLUME = {10},
NUMBER = {1},
PAGES = {165-178},
URL = {http://dx.doi.org/10.1007/s00026-006-0280-z},
NOTE = {http://www.public.iastate.edu/~swillson/Solvability.pdf},
ANNOTE = {BIBUPDATE : 20070924},
KEYWORDS = {from distances, from network, labeling, phylogenetic network, phylogeny}
}

18

Stephen J. Willson. Unique Reconstruction of Tree-Like Phylogenetic Networks from Distances Between Leaves. In BMB, Vol. 68:919-944, 2006.
Keywords: explicit network, from distances, identifiability, mrca network, phylogenetic network, phylogeny, reconstruction.
Note: http://www.public.iastate.edu/~swillson/BMB05-07.rev8.pdf.

@Article{Willson2006b,
AUTHOR = {Willson, Stephen J.},
TITLE = {Unique Reconstruction of Tree-Like Phylogenetic Networks from Distances Between Leaves},
YEAR = {2006},
JOURNAL = {BMB},
VOLUME = {68},
PAGES = {919-944},
URL = {http://dx.doi.org/10.1007/s11538-005-9044-x},
NOTE = {http://www.public.iastate.edu/~swillson/BMB05-07.rev8.pdf},
ANNOTE = {BIBUPDATE : 20070924},
KEYWORDS = {explicit network, from distances, identifiability, mrca network, phylogenetic network, phylogeny, reconstruction}
}

19

Yufeng Wu and Dan Gusfield. Efficient Computation of Minimum Recombination with Genotypes (not Haplotypes) In CSB06, Pages 147-156, 2006.
Note: http://www.lifesciencessociety.org/CSB2006/Papers/131_Wu.pdf.

@InProceedings{WuGusfield2006,
AUTHOR = {Wu, Yufeng and Gusfield, Dan},
TITLE = {Efficient Computation of Minimum Recombination with Genotypes (not Haplotypes)},
YEAR = {2006},
BOOKTITLE = {CSB06},
PAGES = {147-156},
URL = {http://dx.doi.org/10.1142/1860947573_0024},
NOTE = {http://www.lifesciencessociety.org/CSB2006/Papers/131_Wu.pdf},
ANNOTE = {BIBUPDATE : 20070918}
}

20

Esra Erdem, Vladimir Lifschitz and Don Ringe. Temporal phylogenetic networks and logic programming. In Theory and Practice of Logic Programming, Vol. 6:539-558, 2006.
Note: http://arxiv.org/abs/cs/0508129v1.

@Article{ELR2006,
AUTHOR = {Erdem, Esra and Lifschitz, Vladimir and Ringe, Don},
TITLE = {Temporal phylogenetic networks and logic programming},
YEAR = {2006},
JOURNAL = {Theory and Practice of Logic Programming},
VOLUME = {6},
PAGES = {539-558},
URL = {http://dx.doi.org/10.1017/S1471068406002729},
NOTE = {http://arxiv.org/abs/cs/0508129v1},
ANNOTE = {CITE : }
}

21

Bhaskar DasGupta, Sergio Ferrarini, Uthra Gopalakrishnan and Nisha Raj Paryani. Inapproximability results for the lateral gene transfer problem. In JCO, Vol. 11(4):387-405, 2006.
Keywords: approximation, from rooted trees, from species tree, inapproximability, lateral gene transfer, parsimony, phylogenetic network, phylogeny.
Note: http://www.cs.uic.edu/~dasgupta/resume/publ/papers/t-scenario-3-reviewed-3.pdf.

@Article{DFGP2006,
AUTHOR = {DasGupta, Bhaskar and Ferrarini, Sergio and Gopalakrishnan, Uthra and Paryani, Nisha Raj},
TITLE = {Inapproximability results for the lateral gene transfer problem},
YEAR = {2006},
JOURNAL = {JCO},
VOLUME = {11},
NUMBER = {4},
PAGES = {387-405},
URL = {http://dx.doi.org/10.1007/s10878-006-8212-8},
NOTE = {http://www.cs.uic.edu/~dasgupta/resume/publ/papers/t-scenario-3-reviewed-3.pdf},
ANNOTE = {BIBUPDATE : 20071120},
KEYWORDS = {approximation, from rooted trees, from species tree, inapproximability, lateral gene transfer, parsimony, phylogenetic network, phylogeny}
}

22

Robert G. Beiko and Nicholas Hamilton. Phylogenetic identification of lateral genetic transfer events. In BMCEB, Vol. 6(15), 2006.
Keywords: evaluation, from rooted trees, from unrooted trees, lateral gene transfer, Program EEEP, Program HorizStory, Program LatTrans, reconstruction, software, SPR distance.
Note: http://dx.doi.org/10.1186/1471-2148-6-15.

Toggle abstract

@Article{BeikoHamilton2006,
AUTHOR = {Beiko, Robert G. and Hamilton, Nicholas},
TITLE = {Phylogenetic identification of lateral genetic transfer events},
YEAR = {2006},
JOURNAL = {BMCEB},
VOLUME = {6},
NUMBER = {15},
URL = {http://dx.doi.org/10.1186/1471-2148-6-15},
NOTE = {http://dx.doi.org/10.1186/1471-2148-6-15},
ANNOTE = {BIBUPDATE : 20071120},
KEYWORDS = {evaluation, from rooted trees, from unrooted trees, lateral gene transfer, Program EEEP, Program HorizStory, Program LatTrans, reconstruction, software, SPR distance}
}

23

Juan Diego Trujillo and Carlos Cotta. An Evolutionary Approach to the Inference of Phylogenetic Networks. In Proceedings of the ninth Conference on Parallel Problem Solving from Nature (PPSN'IX), Vol. 4193:332-341 of LNCS, springer, 2006.
Note: http://www.lcc.uma.es/~ccottap/papers/trujillo06ppsn.pdf.

@InProceedings{TrujilloCotta2006,
AUTHOR = {Trujillo, Juan Diego and Cotta, Carlos},
TITLE = {An Evolutionary Approach to the Inference of Phylogenetic Networks},
YEAR = {2006},
BOOKTITLE = {Proceedings of the ninth Conference on Parallel Problem Solving from Nature (PPSN'IX)},
VOLUME = {4193},
PAGES = {332-341},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/11844297_34},
NOTE = {http://www.lcc.uma.es/~ccottap/papers/trujillo06ppsn.pdf},
ANNOTE = {BIBUPDATE : 20071121}
}

24

Arvind Gupta, Ján Manuch, Xiaohong Zhao and Ladislav Stacho. Characterization of the existence of galled-tree networks. In JBCB, Vol. 4(6):1309-1328, 2006.
Keywords: characterization, galled tree.
Note: http://www.pims.math.ca/~manuch/papers/characterization_JBCB2006.pdf.

@Article{GMZS2006,
AUTHOR = {Gupta, Arvind and Manuch, J{\~A}�n and Zhao, Xiaohong and Stacho, Ladislav},
TITLE = {Characterization of the existence of galled-tree networks},
YEAR = {2006},
JOURNAL = {JBCB},
VOLUME = {4},
NUMBER = {6},
PAGES = {1309-1328},
URL = {http://dx.doi.org/10.1142/S0219720006002478},
NOTE = {http://www.pims.math.ca/~manuch/papers/characterization_JBCB2006.pdf},
ANNOTE = {CITE : },
KEYWORDS = {characterization, galled tree}
}

25

Mohd Abdul Hai Zahid, Ankush Mittal and Ramesh C. Joshi. A pattern recognition-based approach for phylogenetic network construction with constrained recombination. In Pattern Recognition, Vol. 39:2312-2322, 2006.
Note: http://www.isical.ac.in/~zahid_t/publications/papers/revision 2.pdf.

@Article{ZMJ2006,
AUTHOR = {Zahid, Mohd Abdul Hai and Mittal, Ankush and Joshi, Ramesh C.},
TITLE = {A pattern recognition-based approach for phylogenetic network construction with constrained recombination},
YEAR = {2006},
JOURNAL = {Pattern Recognition},
VOLUME = {39},
PAGES = {2312-2322},
URL = {http://dx.doi.org/10.1016/j.patcog.2006.06.020},
NOTE = {http://www.isical.ac.in/~zahid_t/publications/papers/revision 2.pdf},
ANNOTE = {BIBUPDATE : 20071126}
}

26

Yun S. Song. A Concise Necessary and Sufficient Condition for the Existence of a Galled-Tree. In TCBB, Vol. 3(2):186-191, 2006.
Keywords: characterization, from sequences, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.eecs.berkeley.edu/~yss/Pub/nasc4gall.pdf.

@Article{Song2006,
AUTHOR = {Song, Yun S.},
TITLE = {A Concise Necessary and Sufficient Condition for the Existence of a Galled-Tree},
YEAR = {2006},
JOURNAL = {TCBB},
VOLUME = {3},
NUMBER = {2},
PAGES = {186-191},
URL = {http://dx.doi.org/10.1109/TCBB.2006.15},
NOTE = {http://www.eecs.berkeley.edu/~yss/Pub/nasc4gall.pdf},
ANNOTE = {CITE : },
KEYWORDS = {characterization, from sequences, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction}
}

27

Patricia Buendia and Giri Narasimhan. Serial NetEvolve: A flexible utility for generating serially-sampled sequences along a tree or recombinant network. In BIO, Vol. 18(22):2313-2314, 2006.
Keywords: generation, phylogenetic network, phylogeny, Program Serial NetEvolve, Program Treevolve, recombination, software.
Note: http://dx.doi.org/10.1093/bioinformatics/btl387.

Toggle abstract

@Article{BuendiaNarasimhan2006,
AUTHOR = {Buendia, Patricia and Narasimhan, Giri},
TITLE = {Serial NetEvolve: A flexible utility for generating serially-sampled sequences along a tree or recombinant network},
YEAR = {2006},
JOURNAL = {BIO},
VOLUME = {18},
NUMBER = {22},
PAGES = {2313-2314},
URL = {http://dx.doi.org/10.1093/bioinformatics/btl387},
NOTE = {http://dx.doi.org/10.1093/bioinformatics/btl387},
ANNOTE = {BIBUPDATE : 20071228},
KEYWORDS = {generation, phylogenetic network, phylogeny, Program Serial NetEvolve, Program Treevolve, recombination, software}
}

28

Tetsuo Asano, Patricia Evans, Ryuhei Uehara and Gabriel Valiente. Site Consistency in Phylogenetic Networks with Recombination. In C. S. Iliopoulos, K. Park and K. Steinhöfel editors, Algorithms in Bioinformatics, Vol. 6:15-26 of Texts in Algorithmics, College Publications, 2006.

@InBook{AEUV2006,
AUTHOR = {Asano, Tetsuo and Evans, Patricia and Uehara, Ryuhei and Valiente, Gabriel},
TITLE = {Site Consistency in Phylogenetic Networks with Recombination},
YEAR = {2006},
BOOKTITLE = {Algorithms in Bioinformatics},
VOLUME = {6},
PAGES = {15-26},
EDITOR = {Iliopoulos, C. S. and Park, K. and Steinh{\~A}�fel, K.},
SERIES = {Texts in Algorithmics},
PUBLISHER = {College Publications},
ANNOTE = {BIBUPDATE : 20080505}
}

29

Kim McBreen and Peter J. Lockhart. Reconstructing reticulate evolutionary histories of plants. In Trends in Plant Science, Vol. 11(8):103-122, 2006.
Note: http://www.aseanbiodiversity.info/Abstract/51006032.pdf.

@Article{McBreenLockhart2006,
AUTHOR = {McBreen, Kim and Lockhart, Peter J.},
TITLE = {Reconstructing reticulate evolutionary histories of plants},
YEAR = {2006},
JOURNAL = {Trends in Plant Science},
VOLUME = {11},
NUMBER = {8},
PAGES = {103-122},
URL = {http://dx.doi.org/10.1016/j.tplants.2006.06.004},
NOTE = {http://www.aseanbiodiversity.info/Abstract/51006032.pdf},
ANNOTE = {BIBUPDATE : 20080513}
}

30

Guillaume Bourque and Louxin Zhang. Models and Methods in Comparative Genomics. In Chau-Wen Tseng editor, Advances in Computers, Special Volume: Computational Biology, Vol. 68, Elsevier, 2006.
Keywords: from distances, from rooted trees, from sequences, galled tree, phylogenetic network, phylogeny, survey.
Note: http://www.math.nus.edu.sg/~matzlx/papers/CompGen_ZLX.pdf.

@InBook{BourqueZhang2006,
AUTHOR = {Bourque, Guillaume and Zhang, Louxin},
TITLE = {Models and Methods in Comparative Genomics},
YEAR = {2006},
BOOKTITLE = {Advances in Computers, Special Volume: Computational Biology},
VOLUME = {68},
EDITOR = {Tseng, Chau-Wen},
PUBLISHER = {Elsevier},
URL = {http://dx.doi.org/10.1016/s0065-2458(06)68002-9},
NOTE = {http://www.math.nus.edu.sg/~matzlx/papers/CompGen_ZLX.pdf},
ANNOTE = {BIBUPDATE : 20080605},
KEYWORDS = {from distances, from rooted trees, from sequences, galled tree, phylogenetic network, phylogeny, survey}
}

31

Pawel Górecki. Detection of horizontal gene transfer. PhD thesis, Warsaw University, Poland, 2006.
Keywords: explicit network, from rooted trees, from species tree, lateral gene transfer, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction.

@PhdThesis{Gorecki2006,
AUTHOR = {G{\~A}�recki, Pawel},
TITLE = {Detection of horizontal gene transfer},
YEAR = {2006},
SCHOOL = {Warsaw University, Poland},
ANNOTE = {CITE : },
KEYWORDS = {explicit network, from rooted trees, from species tree, lateral gene transfer, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction}
}

32

Vladimir Makarenkov, Alix Boc, Charles Delwiche, Alpha B. Diallo and Hervé Philippe. New Efficient Algorithm for Modeling Partial and Complete Gene Transfer Scenarios. In IFCS06, Pages 341-349, springer, 2006.
Note: http://www.labunix.uqam.ca/~makarenv/makarenv/IFCS_2006_M_et_al.pdf.

@InProceedings{MBDDP2006,
AUTHOR = {Makarenkov, Vladimir and Boc, Alix and Delwiche, Charles and Diallo, Alpha B. and Philippe, Herv{\~A}�},
TITLE = {New Efficient Algorithm for Modeling Partial and Complete Gene Transfer Scenarios},
YEAR = {2006},
BOOKTITLE = {IFCS06},
PAGES = {341-349},
SERIES = {Studies in Classification, Data Analysis, and Knowledge Organization},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/3-540-34416-0_37},
NOTE = {http://www.labunix.uqam.ca/~makarenv/makarenv/IFCS_2006_M_et_al.pdf}
}

33

Olivier Gauthier. Utilisation de réseaux en analyse phylogénétique. PhD thesis, Université de Montréal, Canada, 2006.
Note: http://igm.univ-mlv.fr/phylnet/PhylogeneticNetworks/docs/GauthierPhdThesis.pdf.

@PhdThesis{Gauthier2006,
AUTHOR = {Gauthier, Olivier},
TITLE = {Utilisation de r{\~A}�seaux en analyse phylog{\~A}�n{\~A}�tique},
YEAR = {2006},
SCHOOL = {Universit{\~A}� de Montr{\~A}�al, Canada},
NOTE = {http://igm.univ-mlv.fr/phylnet/PhylogeneticNetworks/docs/GauthierPhdThesis.pdf}
}

34

Mihaela Baroni and Mike Steel. Accumulation Phylogenies. In ACOM, Vol. 10(1):19-30, 2006.
Keywords: abstract network, from clusters, from distances, phylogenetic network, phylogeny, polynomial, reconstruction, regular network.
Note: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.137.1960.

Toggle abstract

@Article{BaroniSteel2006,
AUTHOR = {Baroni, Mihaela and Steel, Mike},
TITLE = {Accumulation Phylogenies},
YEAR = {2006},
JOURNAL = {ACOM},
VOLUME = {10},
NUMBER = {1},
PAGES = {19-30},
URL = {http://dx.doi.org/10.1007/978-3-642-10631-6_121},
NOTE = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.137.1960},
KEYWORDS = {abstract network, from clusters, from distances, phylogenetic network, phylogeny, polynomial, reconstruction, regular network}
}

2005

1

Vineet Bafna and Vikas Bansal. Improved recombination lower bounds for haplotype data. In RECOMB05, Vol. 3500:569-584 of LNCS, springer, 2005.
Keywords: bound, minimum number, phylogeny, recombination.
Note: http://www.cse.ucsd.edu/users/vbafna/pub/recomblb05.pdf.

@InProceedings{BafnaBansal2005,
AUTHOR = {Bafna, Vineet and Bansal, Vikas},
TITLE = {Improved recombination lower bounds for haplotype data},
YEAR = {2005},
BOOKTITLE = {RECOMB05},
VOLUME = {3500},
PAGES = {569-584},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/11415770_43},
NOTE = {http://www.cse.ucsd.edu/users/vbafna/pub/recomblb05.pdf},
ANNOTE = {CITE : },
KEYWORDS = {bound, minimum number, phylogeny, recombination}
}

2

Sergey Bereg and Kathryn Bean. Constructing Phylogenetic Networks from Trees. In BIBE05, Pages 299-305, 2005.
Keywords: evaluation, from distances, phylogenetic network, phylogeny, Program SplitsTree, Program T REX, reconstruction, split, split network.
Note: http://dx.doi.org/10.1109/BIBE.2005.19.

Toggle abstract

@InProceedings{BeregBean2005,
AUTHOR = {Bereg, Sergey and Bean, Kathryn},
TITLE = {Constructing Phylogenetic Networks from Trees},
YEAR = {2005},
BOOKTITLE = {BIBE05},
PAGES = {299-305},
URL = {http://dx.doi.org/10.1109/BIBE.2005.19},
NOTE = {http://dx.doi.org/10.1109/BIBE.2005.19},
ANNOTE = {BIBUPDATE : 20070924},
KEYWORDS = {evaluation, from distances, phylogenetic network, phylogeny, Program SplitsTree, Program T REX, reconstruction, split, split network}
}

3

Sergey Bereg and Yuanyi Zhang. Phylogenetic Networks Based on the Molecular Clock Hypothesis. In BIBE05, Pages 320-323, 2005.
Note: http://dx.doi.org/10.1109/BIBE.2005.46.

Toggle abstract

@InProceedings{BeregZhang2005,
AUTHOR = {Bereg, Sergey and Zhang, Yuanyi},
TITLE = {Phylogenetic Networks Based on the Molecular Clock Hypothesis},
YEAR = {2005},
BOOKTITLE = {BIBE05},
PAGES = {320-323},
URL = {http://dx.doi.org/10.1109/BIBE.2005.46},
NOTE = {http://dx.doi.org/10.1109/BIBE.2005.46},
ANNOTE = {BIBUPDATE : 20070924}
}

4

Mihaela Baroni, Stefan Grünewald, Vincent Moulton and Charles Semple. Bounding the number of hybridization events for a consistent evolutionary history. In JOMB, Vol. 51(2):171-182, 2005.
Keywords: agreement forest, bound, explicit network, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction, SPR distance.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BGMS05.pdf.

Toggle abstract

@Article{BGMS2005,
AUTHOR = {Baroni, Mihaela and Gr{\~A}�newald, Stefan and Moulton, Vincent and Semple, Charles},
TITLE = {Bounding the number of hybridization events for a consistent evolutionary history},
YEAR = {2005},
JOURNAL = {JOMB},
VOLUME = {51},
NUMBER = {2},
PAGES = {171-182},
URL = {http://dx.doi.org/10.1007/s00285-005-0315-9},
NOTE = {http://www.math.canterbury.ac.nz/~c.semple/papers/BGMS05.pdf},
ANNOTE = {CITE : },
KEYWORDS = {agreement forest, bound, explicit network, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction, SPR distance}
}

5

Magnus Bordewich and Charles Semple. On the computational complexity of the rooted subtree prune and regraft distance. In ACOM, Vol. 8:409-423, 2005.
Keywords: agreement forest, from rooted trees, NP complete, SPR distance.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BS04.pdf.

Toggle abstract

@Article{BordewichSemple2005,
AUTHOR = {Bordewich, Magnus and Semple, Charles},
TITLE = {On the computational complexity of the rooted subtree prune and regraft distance},
YEAR = {2005},
JOURNAL = {ACOM},
VOLUME = {8},
PAGES = {409-423},
URL = {http://dx.doi.org/10.1007/s00026-004-0229-z},
NOTE = {http://www.math.canterbury.ac.nz/~c.semple/papers/BS04.pdf},
ANNOTE = {BIBUPDATE : 20070919},
KEYWORDS = {agreement forest, from rooted trees, NP complete, SPR distance}
}

6

Ho-Leung Chan, Jesper Jansson, Tak-Wah Lam and Siu-Ming Yiu. Reconstructing an Ultrametric Galled Phylogenetic Network from a Distance Matrix. In MFCS05, Vol. 3618:224-235 of LNCS, springer, 2005.
Keywords: from distances, galled tree, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1007/11549345_20.

@InProceedings{CJLY2005,
AUTHOR = {Chan, Ho-Leung and Jansson, Jesper and Lam, Tak-Wah and Yiu, Siu-Ming},
TITLE = {Reconstructing an Ultrametric Galled Phylogenetic Network from a Distance Matrix},
YEAR = {2005},
BOOKTITLE = {MFCS05},
VOLUME = {3618},
PAGES = {224-235},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/11549345_20},
NOTE = {http://dx.doi.org/10.1007/11549345_20},
ANNOTE = {CITE : },
KEYWORDS = {from distances, galled tree, phylogenetic network, phylogeny, reconstruction}
}

7

Charles Choy, Jesper Jansson, Kunihiko Sadakane and Wing-Kin Sung. Computing the maximum agreement of phylogenetic networks. In TCS, Vol. 335(1):93-107, 2005.
Keywords: dynamic programming, FPT, level k phylogenetic network, MASN, NP complete, phylogenetic network, phylogeny.
Note: http://www.df.lth.se/~jj/Publications/masn8_TCS2005.pdf.

Toggle abstract

@Article{CJSS2005,
AUTHOR = {Choy, Charles and Jansson, Jesper and Sadakane, Kunihiko and Sung, Wing-Kin},
TITLE = {Computing the maximum agreement of phylogenetic networks},
YEAR = {2005},
JOURNAL = {TCS},
VOLUME = {335},
NUMBER = {1},
PAGES = {93-107},
URL = {http://dx.doi.org/10.1016/j.tcs.2004.12.012},
NOTE = {http://www.df.lth.se/~jj/Publications/masn8_TCS2005.pdf},
ANNOTE = {CITE : },
KEYWORDS = {dynamic programming, FPT, level k phylogenetic network, MASN, NP complete, phylogenetic network, phylogeny}
}

8

Elena Dubrova. Phylogenetic networks with edge-disjoint recombination cycles. In Proceedings of SPIE Bioengineered and Bioinspired Systems II (SPIE-BBS II), Vol. 5839:381-388, 2005.
Keywords: galled tree, phylogenetic network, polynomial, site consistency.
Note: http://dx.doi.org/10.1117/12.607910.

Toggle abstract

@InProceedings{Dubrova2005,
AUTHOR = {Dubrova, Elena},
TITLE = {Phylogenetic networks with edge-disjoint recombination cycles},
YEAR = {2005},
BOOKTITLE = {Proceedings of SPIE Bioengineered and Bioinspired Systems II (SPIE-BBS II)},
VOLUME = {5839},
PAGES = {381-388},
URL = {http://dx.doi.org/10.1117/12.607910},
NOTE = {http://dx.doi.org/10.1117/12.607910},
ANNOTE = {CITE : },
KEYWORDS = {galled tree, phylogenetic network, polynomial, site consistency}
}

9

Dan Gusfield. On the Full-Decomposition Optimality Conjecture for Phylogenetic Networks. 2005.
Keywords: characterization, explicit network, from sequences, phylogenetic network, reconstruction.
Note: UC Davis Computer Science Technical Report CSE-2005, http://wwwcsif.cs.ucdavis.edu/~gusfield/fullydecomp.pdf.

@Misc{Gusfield2005,
AUTHOR = {Gusfield, Dan},
TITLE = {On the Full-Decomposition Optimality Conjecture for Phylogenetic Networks},
YEAR = {2005},
NOTE = {UC Davis Computer Science Technical Report CSE-2005, http://wwwcsif.cs.ucdavis.edu/~gusfield/fullydecomp.pdf},
ANNOTE = {BIBUPDATE : 20070914},
KEYWORDS = {characterization, explicit network, from sequences, phylogenetic network, reconstruction}
}

10

Dan Gusfield and Vikas Bansal. A Fundamental Decomposition Theory for Phylogenetic Networks and Incompatible Characters. In RECOMB05, Vol. 3500:217-232 of LNCS, springer, 2005.
Keywords: explicit network, from sequences, phylogenetic network, phylogeny, polynomial, recombination, reconstruction.
Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/gusfieldrecomb.pdf.

@InProceedings{GusfieldBansal2005,
AUTHOR = {Gusfield, Dan and Bansal, Vikas},
TITLE = {A Fundamental Decomposition Theory for Phylogenetic Networks and Incompatible Characters},
YEAR = {2005},
BOOKTITLE = {RECOMB05},
VOLUME = {3500},
PAGES = {217-232},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/11415770_17},
NOTE = {http://wwwcsif.cs.ucdavis.edu/~gusfield/gusfieldrecomb.pdf},
ANNOTE = {BIBUPDATE : 20070914},
KEYWORDS = {explicit network, from sequences, phylogenetic network, phylogeny, polynomial, recombination, reconstruction}
}

11

Barbara R. Holland, Frédéric Delsuc and Vincent Moulton. Visualizing Conflicting Evolutionary Hypotheses in Large Collections of Trees: Using Consensus Networks to Study the Origins of Placentals and Hexapods. In Systematic Biology, Vol. 54(1):66-76, 2005.
Keywords: consensus.
Note: http://hal-sde.archives-ouvertes.fr/halsde-00193050/fr/.

Toggle abstract

@Article{HDM2005,
AUTHOR = {Holland, Barbara R. and Delsuc, Fr{\~A}�d{\~A}�ric and Moulton, Vincent},
TITLE = {Visualizing Conflicting Evolutionary Hypotheses in Large Collections of Trees: Using Consensus Networks to Study the Origins of Placentals and Hexapods},
YEAR = {2005},
JOURNAL = {Systematic Biology},
VOLUME = {54},
NUMBER = {1},
PAGES = {66-76},
URL = {http://dx.doi.org/10.1080/10635150590906055},
NOTE = {http://hal-sde.archives-ouvertes.fr/halsde-00193050/fr/},
ANNOTE = {BIBUPDATE : 20070920},
KEYWORDS = {consensus}
}

12

Ying-Jun He, Trinh N. D. Huynh, Jesper Jansson and Wing-Kin Sung. Inferring Phylogenetic Relationships Avoiding Forbidden Rooted Triplets. In APBC05, Pages 339-348, 2005.
Note: https://dflund.se/~jj/Publications/forb_triplets4_APBC2005.pdf.

@InProceedings{HHJS2005,
AUTHOR = {He, Ying-Jun and Huynh, Trinh N. D. and Jansson, Jesper and Sung, Wing-Kin},
TITLE = {Inferring Phylogenetic Relationships Avoiding Forbidden Rooted Triplets},
YEAR = {2005},
BOOKTITLE = {APBC05},
PAGES = {339-348},
NOTE = {https://dflund.se/~jj/Publications/forb_triplets4_APBC2005.pdf},
ANNOTE = {BIBUPDATE : 20070917}
}

13

Trinh N. D. Huynh, Jesper Jansson, Nguyen Bao Nguyen and Wing-Kin Sung. Constructing a Smallest Refining Galled Phylogenetic Network. In RECOMB05, Vol. 3500:265-280 of LNCS, springer, 2005.
Keywords: from rooted trees, galled tree, NP complete, phylogenetic network, phylogeny, polynomial, Program SPNet, reconstruction.
Note: http://www.df.lth.se/~jj/Publications/refining_gn3_RECOMB2005.pdf.

@InProceedings{HJNS2005,
AUTHOR = {Huynh, Trinh N. D. and Jansson, Jesper and Nguyen, Nguyen Bao and Sung, Wing-Kin},
TITLE = {Constructing a Smallest Refining Galled Phylogenetic Network},
YEAR = {2005},
BOOKTITLE = {RECOMB05},
VOLUME = {3500},
PAGES = {265-280},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/11415770_20},
NOTE = {http://www.df.lth.se/~jj/Publications/refining_gn3_RECOMB2005.pdf},
ANNOTE = {BIBUPDATE : 20070924},
KEYWORDS = {from rooted trees, galled tree, NP complete, phylogenetic network, phylogeny, polynomial, Program SPNet, reconstruction}
}

14

Daniel H. Huson, Tobias Kloepper, Peter J. Lockhart and Mike Steel. Reconstruction of Reticulate Networks from Gene Trees. In RECOMB05, Vol. 3500:233-249 of LNCS, springer, 2005.
Keywords: from rooted trees, from splits, phylogenetic network, phylogeny, reconstruction, split, split network, visualization.
Note: http://dx.doi.org/10.1007/11415770_18.

@InProceedings{HKLS2005,
AUTHOR = {Huson, Daniel H. and Kloepper, Tobias and Lockhart, Peter J. and Steel, Mike},
TITLE = {Reconstruction of Reticulate Networks from Gene Trees},
YEAR = {2005},
BOOKTITLE = {RECOMB05},
VOLUME = {3500},
PAGES = {233-249},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/11415770_18},
NOTE = {http://dx.doi.org/10.1007/11415770_18},
ANNOTE = {CITE : },
KEYWORDS = {from rooted trees, from splits, phylogenetic network, phylogeny, reconstruction, split, split network, visualization}
}

15

Jotun Hein, Mikkel H. Schierup and Carsten Wiuf. The coalescent with recombination. In Gene Genealogies, Variation and Evolution, Pages 127-171, Oxford University Press, 2005.

@InBook{HSW2005,
AUTHOR = {Hein, Jotun and Schierup, Mikkel H. and Wiuf, Carsten},
TITLE = {The coalescent with recombination},
YEAR = {2005},
BOOKTITLE = {Gene Genealogies, Variation and Evolution},
PAGES = {127-171},
PUBLISHER = {Oxford University Press},
ANNOTE = {CITE : }
}

16

Daniel H. Huson and Tobias Kloepper. Computing recombination networks from binary sequences. In ECCB05, Vol. 21(suppl. 2):ii159-ii165 of BIO, 2005.
Keywords: from sequences, phylogenetic network, phylogeny, recombination.
Note: http://dx.doi.org/10.1093/bioinformatics/bti1126.

Toggle abstract

@InProceedings{HusonKloepper2005,
AUTHOR = {Huson, Daniel H. and Kloepper, Tobias},
TITLE = {Computing recombination networks from binary sequences},
YEAR = {2005},
BOOKTITLE = {ECCB05},
VOLUME = {21},
NUMBER = {suppl. 2},
PAGES = {ii159-ii165},
SERIES = {BIO},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti1126},
NOTE = {http://dx.doi.org/10.1093/bioinformatics/bti1126},
ANNOTE = {CITE : },
KEYWORDS = {from sequences, phylogenetic network, phylogeny, recombination}
}

17

Jesper Jansson and Wing-Kin Sung. The Maximum Agreement of Two Nested Phylogenetic Networks. In ISAAC04, Vol. 3341:581-593 of LNCS, springer, 2005.
Keywords: dynamic programming, MASN, nested network, NP complete, phylogenetic network, phylogeny, polynomial.
Note: http://www.df.lth.se/~jj/Publications/nested7_ISAAC2004.pdf.

@InProceedings{JanssonSung2004a,
AUTHOR = {Jansson, Jesper and Sung, Wing-Kin},
TITLE = {The Maximum Agreement of Two Nested Phylogenetic Networks},
YEAR = {2005},
BOOKTITLE = {ISAAC04},
VOLUME = {3341},
PAGES = {581-593},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-540-30551-4_51},
NOTE = {http://www.df.lth.se/~jj/Publications/nested7_ISAAC2004.pdf},
ANNOTE = {BIBUPDATE : 20070924},
KEYWORDS = {dynamic programming, MASN, nested network, NP complete, phylogenetic network, phylogeny, polynomial}
}

18

Jesper Jansson, Nguyen Bao Nguyen and Wing-Kin Sung. Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network. In SODA05, Pages 349-358, 2005.
Keywords: approximation, explicit network, from triplets, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://portal.acm.org/citation.cfm?id=1070481.

@InProceedings{JNS2005,
AUTHOR = {Jansson, Jesper and Nguyen, Nguyen Bao and Sung, Wing-Kin},
TITLE = {Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network},
YEAR = {2005},
BOOKTITLE = {SODA05},
PAGES = {349-358},
URL = {http://doi.acm.org/10.1145/1070432.1070481},
NOTE = {http://portal.acm.org/citation.cfm?id=1070481},
KEYWORDS = {approximation, explicit network, from triplets, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction}
}

19

Victor Kunin, Leon Goldovsky, Nikos Darzentas and Christos A. Ouzounis. The net of life: Reconstructing the microbial phylogenetic network. In GR, Vol. 15:954-959, 2005.
Note: http://dx.doi.org/10.1101/gr.3666505.

Toggle abstract

@Article{KGDO2005,
AUTHOR = {Kunin, Victor and Goldovsky, Leon and Darzentas, Nikos and Ouzounis, Christos A.},
TITLE = {The net of life: Reconstructing the microbial phylogenetic network},
YEAR = {2005},
JOURNAL = {GR},
VOLUME = {15},
PAGES = {954-959},
URL = {http://dx.doi.org/10.1101/gr.3666505},
NOTE = {http://dx.doi.org/10.1101/gr.3666505},
ANNOTE = {CITE : }
}

20

Martyn Kennedy, Barbara R. Holland, Russel D. Gray and Hamish G. Spencer. Untangling Long Branches: Identifying Conflicting Phylogenetic Signals Using Spectral Analysis, Neighbor-Net, and Consensus Networks. In Systematic Biology, Vol. 54(4):620-633, 2005.
Keywords: abstract network, consensus, NeighborNet, phylogenetic network, phylogeny.
Note: http://awcmee.massey.ac.nz/people/bholland/pdf/Kennedy_etal_2005.pdf.

@Article{KHGS2005,
AUTHOR = {Kennedy, Martyn and Holland, Barbara R. and Gray, Russel D. and Spencer, Hamish G.},
TITLE = {Untangling Long Branches: Identifying Conflicting Phylogenetic Signals Using Spectral Analysis, Neighbor-Net, and Consensus Networks},
YEAR = {2005},
JOURNAL = {Systematic Biology},
VOLUME = {54},
NUMBER = {4},
PAGES = {620-633},
URL = {http://dx.doi.org/10.1080/106351591007462},
NOTE = {http://awcmee.massey.ac.nz/people/bholland/pdf/Kennedy_etal_2005.pdf},
ANNOTE = {BIBUPDATE : 20070920},
KEYWORDS = {abstract network, consensus, NeighborNet, phylogenetic network, phylogeny}
}

21

Rune Lyngsø, Yun S. Song and Jotun Hein. Minimum Recombination Histories by Branch and Bound. In WABI05, Vol. 3692:239-250 of LNCS, springer, 2005.
Keywords: ARG, branch and bound, from sequences, minimum number, Program Beagle, recombination, reconstruction, software.
Note: http://www.cs.ucdavis.edu/~yssong/Pub/WABI05-239.pdf.

@InProceedings{LSH2005,
AUTHOR = {Lyngs{\~A}�, Rune and Song, Yun S. and Hein, Jotun},
TITLE = {Minimum Recombination Histories by Branch and Bound},
YEAR = {2005},
BOOKTITLE = {WABI05},
VOLUME = {3692},
PAGES = {239-250},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/11557067_20},
NOTE = {http://www.cs.ucdavis.edu/~yssong/Pub/WABI05-239.pdf},
ANNOTE = {CITE : },
KEYWORDS = {ARG, branch and bound, from sequences, minimum number, Program Beagle, recombination, reconstruction, software}
}

22

David A. Morrison. Networks in phylogenetic analysis: new tools for population biology. In IJP, Vol. 35:567-582, 2005.
Keywords: median network, NeighborNet, phylogenetic network, phylogeny, population genetics, Program Network, Program Spectronet, Program SplitsTree, Program T REX, Program TCS, reconstruction, reticulogram, split decomposition, survey.
Note: http://hem.fyristorg.com/acacia/papers/networks.pdf.

@Article{Morrison2005,
AUTHOR = {Morrison, David A.},
TITLE = {Networks in phylogenetic analysis: new tools for population biology},
YEAR = {2005},
JOURNAL = {IJP},
VOLUME = {35},
PAGES = {567-582},
URL = {http://dx.doi.org/10.1016/j.ijpara.2005.02.007},
NOTE = {http://hem.fyristorg.com/acacia/papers/networks.pdf},
ANNOTE = {CITE : },
KEYWORDS = {median network, NeighborNet, phylogenetic network, phylogeny, population genetics, Program Network, Program Spectronet, Program SplitsTree, Program T REX, Program TCS, reconstruction, reticulogram, split decomposition, survey}
}

23

Vincent Moulton and Katharina Huber. Phylogenetic Networks. In Olivier Gascuel editor, Mathematics of evolution and phylogeny, Pages 178-200, Oxford University Press, 2005.

@InBook{MoultonHuber2005,
AUTHOR = {Moulton, Vincent and Huber, Katharina},
TITLE = {Phylogenetic Networks},
YEAR = {2005},
BOOKTITLE = {Mathematics of evolution and phylogeny},
PAGES = {178-200},
EDITOR = {Gascuel, Olivier},
PUBLISHER = {Oxford University Press},
ANNOTE = {BIBUPDATE : 20070924}
}

24

Luay Nakhleh and Li-San Wang. Phylogenetic Networks, Trees, and Clusters. In IWBRA05, Vol. 3515:919-926 of LNCS, springer, 2005.
Keywords: cluster containment, evaluation, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, tree containment, tree-child network.
Note: http://www.cs.rice.edu/~nakhleh/Papers/NakhlehWang.pdf.

@InProceedings{NakhlehWang2005a,
AUTHOR = {Nakhleh, Luay and Wang, Li-San},
TITLE = {Phylogenetic Networks, Trees, and Clusters},
YEAR = {2005},
BOOKTITLE = {IWBRA05},
VOLUME = {3515},
PAGES = {919-926},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/11428848_117},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/NakhlehWang.pdf},
ANNOTE = {BIBUPDATE : 20070917},
KEYWORDS = {cluster containment, evaluation, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, tree containment, tree-child network}
}

25

Luay Nakhleh and Li-San Wang. Phylogenetic Networks: Properties and Relationship to Trees and Clusters. In TCSB2, Vol. 3680:82-99 of LNCS, springer, 2005.
Keywords: cluster containment, evaluation, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, tree containment, tree-child network.
Note: http://www.cs.rice.edu/~nakhleh/Papers/LNCS_TCSB05.pdf.

@InProceedings{NakhlehWang2005b,
AUTHOR = {Nakhleh, Luay and Wang, Li-San},
TITLE = {Phylogenetic Networks: Properties and Relationship to Trees and Clusters},
YEAR = {2005},
BOOKTITLE = {TCSB2},
VOLUME = {3680},
PAGES = {82-99},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/11567752_6},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/LNCS_TCSB05.pdf},
ANNOTE = {BIBUPDATE : 20070917},
KEYWORDS = {cluster containment, evaluation, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, tree containment, tree-child network}
}

26

Luay Nakhleh, Guohua Jin, Fengmei Zhao and John Mellor-Crummey. Reconstructing Phylogenetic Networks Using Maximum Parsimony. In CSB05, Pages 93-102, 2005.
Keywords: parsimony, phylogenetic network, phylogeny, Program Nepal, reconstruction.
Note: http://www.cs.rice.edu/~nakhleh/Papers/CSB05.pdf.

@InProceedings{NJZM2005,
AUTHOR = {Nakhleh, Luay and Jin, Guohua and Zhao, Fengmei and Mellor-Crummey, John},
TITLE = {Reconstructing Phylogenetic Networks Using Maximum Parsimony},
YEAR = {2005},
BOOKTITLE = {CSB05},
PAGES = {93-102},
URL = {http://dx.doi.org/10.1109/csb.2005.47},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/CSB05.pdf},
ANNOTE = {CITE : },
KEYWORDS = {parsimony, phylogenetic network, phylogeny, Program Nepal, reconstruction}
}

27

Cam Thach Nguyen, Nguyen Bao Nguyen and Wing-Kin Sung. Fast Algorithms for computing the Tripartition-based Distance between Phylogenetic Networks. In ISAAC05, Pages 402-411, 2005.
Keywords: distance between networks, phylogenetic network, phylogeny, tripartition distance.
Note: http://www.cs.washington.edu/homes/ncthach/Papers/ISAAC2006.pdf.

@InProceedings{NNS2005,
AUTHOR = {Nguyen, Cam Thach and Nguyen, Nguyen Bao and Sung, Wing-Kin},
TITLE = {Fast Algorithms for computing the Tripartition-based Distance between Phylogenetic Networks},
YEAR = {2005},
BOOKTITLE = {ISAAC05},
PAGES = {402-411},
URL = {http://dx.doi.org/10.1007/11602613_41},
NOTE = {http://www.cs.washington.edu/homes/ncthach/Papers/ISAAC2006.pdf},
ANNOTE = {BIBUPDATE : 20070924},
KEYWORDS = {distance between networks, phylogenetic network, phylogeny, tripartition distance}
}

28

Luay Nakhleh, Derek Ruths and Li-San Wang. RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer. In COCOON05, Vol. 3595:84-93 of LNCS, springer, 2005.
Keywords: from rooted trees, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program PhyloNet.
Note: http://www.cs.rice.edu/~nakhleh/Papers/COCOON05.pdf.

@InProceedings{NRW2005a,
AUTHOR = {Nakhleh, Luay and Ruths, Derek and Wang, Li-San},
TITLE = {RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer},
YEAR = {2005},
BOOKTITLE = {COCOON05},
VOLUME = {3595},
PAGES = {84-93},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/11533719_11},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/COCOON05.pdf},
ANNOTE = {BIBUPDATE : 20070917},
KEYWORDS = {from rooted trees, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program PhyloNet}
}

29

Luay Nakhleh, Tandy Warnow, C. Randal Linder and Katherine St. John. Reconstructing reticulate evolution in species - theory and practice. In JCB, Vol. 12(6):796-811, 2005.
Keywords: from rooted trees, galled tree, phylogenetic network, phylogeny, polynomial, Program SPNet, reconstruction, software.
Note: http://www.cs.rice.edu/~nakhleh/Papers/NWLSjcb.pdf.

@Article{NWLS2005,
AUTHOR = {Nakhleh, Luay and Warnow, Tandy and Linder, C. Randal and St. John, Katherine},
TITLE = {Reconstructing reticulate evolution in species - theory and practice},
YEAR = {2005},
JOURNAL = {JCB},
VOLUME = {12},
NUMBER = {6},
PAGES = {796-811},
URL = {http://dx.doi.org/10.1089/cmb.2005.12.796},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/NWLSjcb.pdf},
ANNOTE = {BIBUPDATE : 20071002},
KEYWORDS = {from rooted trees, galled tree, phylogenetic network, phylogeny, polynomial, Program SPNet, reconstruction, software}
}

30

Derek Ruths and Luay Nakhleh. Recombination and phylogeny: effects and detection. In IJBRA, Pages 202-212, 2005.
Note: http://www.cs.rice.edu/~nakhleh/Papers/IJBRA05.pdf.

@Article{RuthsNakhleh2005,
AUTHOR = {Ruths, Derek and Nakhleh, Luay},
TITLE = {Recombination and phylogeny: effects and detection},
YEAR = {2005},
JOURNAL = {IJBRA},
PAGES = {202-212},
URL = {http://dx.doi.org/10.1504/ijbra.2005.007578},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/IJBRA05.pdf},
ANNOTE = {BIBUPDATE : 20070918}
}

31

Yun S. Song and Jotun Hein. Constructing Minimal Ancestral Recombination Graphs. In JCB, Vol. 12(2):147-169, 2005.
Keywords: ARG, minimum number, recombination.
Note: http://www.eecs.berkeley.edu/~yss/Pub/SH-JCB05.pdf.

@Article{SongHein2005,
AUTHOR = {Song, Yun S. and Hein, Jotun},
TITLE = {Constructing Minimal Ancestral Recombination Graphs},
YEAR = {2005},
JOURNAL = {JCB},
VOLUME = {12},
NUMBER = {2},
PAGES = {147-169},
URL = {http://dx.doi.org/10.1089/cmb.2005.12.147},
NOTE = {http://www.eecs.berkeley.edu/~yss/Pub/SH-JCB05.pdf},
ANNOTE = {CITE : },
KEYWORDS = {ARG, minimum number, recombination}
}

32

Yun S. Song, Yufeng Wu and Dan Gusfield. Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution. In ISMB05, Vol. 21:i413-i422 of BIO, 2005.
Keywords: integer linear programming, minimum number, Program HapBound, Program SHRUB, recombination.
Note: http://dx.doi.org/10.1093/bioinformatics/bti1033.

Toggle abstract

@InProceedings{SWG2005,
AUTHOR = {Song, Yun S. and Wu, Yufeng and Gusfield, Dan},
TITLE = {Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution},
YEAR = {2005},
BOOKTITLE = {ISMB05},
VOLUME = {21},
PAGES = {i413-i422},
SERIES = {BIO},
URL = {http://dx.doi.org/10.1093/bioinformatics/bti1033},
NOTE = {http://dx.doi.org/10.1093/bioinformatics/bti1033},
ANNOTE = {BIBUPDATE : 20070918},
KEYWORDS = {integer linear programming, minimum number, Program HapBound, Program SHRUB, recombination}
}

33

Richard C. Winkworth, David Bryant, Peter J. Lockhart, David Havell and Vincent Moulton. Biogeographic Interpretation of Splits Graphs: Least Squares Optimization of Branch Lengths. In Systematic Biology, Vol. 54(1):56-65, 2005.
Keywords: abstract network, from distances, from network, phylogenetic network, phylogeny, reconstruction, split, split network.
Note: http://www.math.auckland.ac.nz/~bryant/Papers/05Biogeographic.pdf.

@Article{WBLHM2005,
AUTHOR = {Winkworth, Richard C. and Bryant, David and Lockhart, Peter J. and Havell, David and Moulton, Vincent},
TITLE = {Biogeographic Interpretation of Splits Graphs: Least Squares Optimization of Branch Lengths},
YEAR = {2005},
JOURNAL = {Systematic Biology},
VOLUME = {54},
NUMBER = {1},
PAGES = {56-65},
URL = {http://dx.doi.org/10.1080/10635150590906046},
NOTE = {http://www.math.auckland.ac.nz/~bryant/Papers/05Biogeographic.pdf},
ANNOTE = {CITE : },
KEYWORDS = {abstract network, from distances, from network, phylogenetic network, phylogeny, reconstruction, split, split network}
}

34

Bhaskar DasGupta, Sergio Ferrarini, Uthra Gopalakrishnan and Nisha Raj Paryani. Inapproximability results for the lateral gene transfer problem. In Proceedings of the Ninth Italian Conference on Theoretical Computer Science (ICTCS'05), Pages 182-195, springer, 2005.
Keywords: approximation, from rooted trees, from species tree, inapproximability, lateral gene transfer, parsimony, phylogenetic network, phylogeny.
Note: http://www.cs.uic.edu/~dasgupta/resume/publ/papers/ictcs-final.pdf.

@InProceedings{DFGP2005,
AUTHOR = {DasGupta, Bhaskar and Ferrarini, Sergio and Gopalakrishnan, Uthra and Paryani, Nisha Raj},
TITLE = {Inapproximability results for the lateral gene transfer problem},
YEAR = {2005},
BOOKTITLE = {Proceedings of the Ninth Italian Conference on Theoretical Computer Science (ICTCS'05)},
PAGES = {182-195},
SERIES = {lncs},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/11560586_15},
NOTE = {http://www.cs.uic.edu/~dasgupta/resume/publ/papers/ictcs-final.pdf},
ANNOTE = {BIBUPDATE : 20071120},
KEYWORDS = {approximation, from rooted trees, from species tree, inapproximability, lateral gene transfer, parsimony, phylogenetic network, phylogeny}
}

35

Dave MacLeod, Robert L. Charlebois, W. Ford Doolittle and Eric Bapteste. Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement. In BMCEB, Vol. 5(27), 2005.
Keywords: explicit network, from rooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program HorizStory, reconstruction, software.
Note: http://dx.doi.org/10.1186/1471-2148-5-27.

Toggle abstract

@Article{MCDB2005,
AUTHOR = {MacLeod, Dave and Charlebois, Robert L. and Doolittle, W. Ford and Bapteste, Eric},
TITLE = {Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement},
YEAR = {2005},
JOURNAL = {BMCEB},
VOLUME = {5},
NUMBER = {27},
URL = {http://dx.doi.org/10.1186/1471-2148-5-27},
NOTE = {http://dx.doi.org/10.1186/1471-2148-5-27},
ANNOTE = {BIBUPDATE : 20071120},
KEYWORDS = {explicit network, from rooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program HorizStory, reconstruction, software}
}

36

Insa Cassens, Patrick Mardulyn and Michel C. Milinkovitch. Evaluating Intraspecific Network Construction Methods Using Simulated Sequence Data: Do Existing Algorithms Outperform the Global Maximum Parsimony Approach? In Systematic Biology, Vol. 54(3):363-372, 2005.
Keywords: abstract network, evaluation, from unrooted trees, haplotype network, parsimony, phylogenetic network, phylogeny, Program Arlequin, Program CombineTrees, Program Network, Program TCS, reconstruction, software.
Note: http://www.lanevol.org/LANE/publications_files/Cassens_etal_SystBio_2005.pdf.

@Article{CMM2005,
AUTHOR = {Cassens, Insa and Mardulyn, Patrick and Milinkovitch, Michel C.},
TITLE = {Evaluating Intraspecific Network Construction Methods Using Simulated Sequence Data: Do Existing Algorithms Outperform the Global Maximum Parsimony Approach?},
YEAR = {2005},
JOURNAL = {Systematic Biology},
VOLUME = {54},
NUMBER = {3},
PAGES = {363-372},
URL = {http://www.jstor.org/stable/20061240},
NOTE = {http://www.lanevol.org/LANE/publications_files/Cassens_etal_SystBio_2005.pdf},
ANNOTE = {CITE : },
KEYWORDS = {abstract network, evaluation, from unrooted trees, haplotype network, parsimony, phylogenetic network, phylogeny, Program Arlequin, Program CombineTrees, Program Network, Program TCS, reconstruction, software}
}

37

David Bryant. Extending tree models to splits networks. In Lior Pachter and Bernd Sturmfels editors, Algebraic Statistics for Computational Biology, Pages 322-334, Cambridge University Press, 2005.
Keywords: abstract network, from splits, likelihood, phylogenetic network, phylogeny, split, split network, statistical model.
Note: http://www.math.auckland.ac.nz/~bryant/Papers/05ascbChapter.pdf.

@InBook{Bryant2005,
AUTHOR = {Bryant, David},
TITLE = {Extending tree models to splits networks},
YEAR = {2005},
BOOKTITLE = {Algebraic Statistics for Computational Biology},
PAGES = {322-334},
EDITOR = {Pachter, Lior and Sturmfels, Bernd},
PUBLISHER = {Cambridge University Press},
URL = {http://dx.doi.org/10.1017/cbo9780511610684.021},
NOTE = {http://www.math.auckland.ac.nz/~bryant/Papers/05ascbChapter.pdf},
ANNOTE = {BIBUPDATE : 20080321},
KEYWORDS = {abstract network, from splits, likelihood, phylogenetic network, phylogeny, split, split network, statistical model}
}

38

Bastienne Vriesendorp and Freek T. Bakker. Reconstructing patterns of reticulate evolution in angiosperms: what can we do? In Taxon, Vol. 54(3):593-604, 2005.
Note: results cited in http://library.wur.nl/wda/dissertations/dis4239.pdf.

@Article{VriesendorpBakker2005,
AUTHOR = {Vriesendorp, Bastienne and Bakker, Freek T.},
TITLE = {Reconstructing patterns of reticulate evolution in angiosperms: what can we do?},
YEAR = {2005},
JOURNAL = {Taxon},
VOLUME = {54},
NUMBER = {3},
PAGES = {593-604},
URL = {http://dx.doi.org/10.2307/25065417},
NOTE = {results cited in http://library.wur.nl/wda/dissertations/dis4239.pdf},
ANNOTE = {CITE : }
}

39

Mohd Abdul Hai Zahid, Ankush Mittal and Ramesh C. Joshi. A Classification Based Approach for Root Unknown Phylogenetic Networks under Constrained Recombination. In Proceedings of the Second International Conference on Distributed Computing and Internet Technology (ICDCIT'05), Vol. 3816:592-603, 2005.
Note: http://www.isical.ac.in/~zahid_t/publications/papers/paper_ICDCIT.pdf.

@InProceedings{ZMJ2005a,
AUTHOR = {Zahid, Mohd Abdul Hai and Mittal, Ankush and Joshi, Ramesh C.},
TITLE = {A Classification Based Approach for Root Unknown Phylogenetic Networks under Constrained Recombination},
YEAR = {2005},
BOOKTITLE = {Proceedings of the Second International Conference on Distributed Computing and Internet Technology (ICDCIT'05)},
VOLUME = {3816},
PAGES = {592-603},
URL = {http://dx.doi.org/10.1007/11604655_66},
NOTE = {http://www.isical.ac.in/~zahid_t/publications/papers/paper_ICDCIT.pdf},
ANNOTE = {BIBUPDATE : 20081101}
}

40

Dung Nguyen, Alix Boc and Vladimir Makarenkov. HGT-Simulator : logiciel pour simuler des transferts horizontaux. In SFC05, 2005.
Note: http://lacim.uqam.ca/~sfc05/Articles/Nguyen_%20Boc_Makarenkov.pdf.

@InProceedings{NBM2005,
AUTHOR = {Nguyen, Dung and Boc, Alix and Makarenkov, Vladimir},
TITLE = {HGT-Simulator : logiciel pour simuler des transferts horizontaux},
YEAR = {2005},
BOOKTITLE = {SFC05},
NOTE = {http://lacim.uqam.ca/~sfc05/Articles/Nguyen_%20Boc_Makarenkov.pdf}
}

41

Derek Ruths. Applications of phylogenetic incongruence to detecting and reconstructing interspecific recombination and horizontal gene transfer. Master's thesis, Rice University, U.S.A., 2005.
Keywords: explicit network, from rooted trees, from species tree, heuristic, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://hdl.handle.net/1911/17912.

@MastersThesis{Ruths2005,
AUTHOR = {Ruths, Derek},
TITLE = {Applications of phylogenetic incongruence to detecting and reconstructing interspecific recombination and horizontal gene transfer},
YEAR = {2005},
SCHOOL = {Rice University, U.S.A.},
NOTE = {http://hdl.handle.net/1911/17912},
KEYWORDS = {explicit network, from rooted trees, from species tree, heuristic, phylogenetic network, phylogeny, polynomial, reconstruction}
}

42

Wei-Shun Su, Tso-Ching Lee and Yaw-Ling Lin. Efficient Algorithms for Constructing Phylogenetic Networks with Restricted Recombinations. In NCS05, Pages 1-7, 2005.
Keywords: explicit network, from sequences, phylogenetic network, phylogeny, reconstruction.
Note: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.168.6735.

@InProceedings{SLL2005,
AUTHOR = {Su, Wei-Shun and Lee, Tso-Ching and Lin, Yaw-Ling},
TITLE = {Efficient Algorithms for Constructing Phylogenetic Networks with Restricted Recombinations},
YEAR = {2005},
BOOKTITLE = {NCS05},
PAGES = {1-7},
NOTE = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.168.6735},
KEYWORDS = {explicit network, from sequences, phylogenetic network, phylogeny, reconstruction}
}

2004

1

Vineet Bafna and Vikas Bansal. The Number of Recombination Events in a Sample History: Conflict Graph and Lower Bounds. In TCBB, Vol. 1(2):78-90, 2004.
Keywords: ARG, bound, minimum number, phylogeny, recombination.
Note: http://www-cse.ucsd.edu/users/vbafna/pub/tcbb04.pdf.

Toggle abstract

@Article{BafnaBansal2004,
AUTHOR = {Bafna, Vineet and Bansal, Vikas},
TITLE = {The Number of Recombination Events in a Sample History: Conflict Graph and Lower Bounds},
YEAR = {2004},
JOURNAL = {TCBB},
VOLUME = {1},
NUMBER = {2},
PAGES = {78-90},
URL = {http://dx.doi.org/10.1109/TCBB.2004.23},
NOTE = {http://www-cse.ucsd.edu/users/vbafna/pub/tcbb04.pdf},
ANNOTE = {BIBUPDATE : 20070918},
KEYWORDS = {ARG, bound, minimum number, phylogeny, recombination}
}

2

David Bryant. The Splits in the Neighborhood of a Tree. In ACOM, Vol. 8(1):1-11, 2004.
Note: http://citeseer.ist.psu.edu/668699.html.

@Article{Bryant2004,
AUTHOR = {Bryant, David},
TITLE = {The Splits in the Neighborhood of a Tree},
YEAR = {2004},
JOURNAL = {ACOM},
VOLUME = {8},
NUMBER = {1},
PAGES = {1-11},
URL = {http://dx.doi.org/10.1007/s00026-004-0200-z},
NOTE = {http://citeseer.ist.psu.edu/668699.html},
ANNOTE = {BIBUPDATE : 20070905}
}

3

David Bryant and Vincent Moulton. NeighborNet: An Agglomerative Method for the Construction of Phylogenetic Networks. In MBE, Vol. 21(2):255-265, 2004.
Keywords: phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network.
Note: http://www.math.auckland.ac.nz/~bryant/Papers/04NeighborNet.pdf.

Toggle abstract

@Article{BryantMoulton2004,
AUTHOR = {Bryant, David and Moulton, Vincent},
TITLE = {NeighborNet: An Agglomerative Method for the Construction of Phylogenetic Networks},
YEAR = {2004},
JOURNAL = {MBE},
VOLUME = {21},
NUMBER = {2},
PAGES = {255-265},
URL = {http://dx.doi.org/10.1093/molbev/msh018},
NOTE = {http://www.math.auckland.ac.nz/~bryant/Papers/04NeighborNet.pdf},
ANNOTE = {BIBUPDATE : 20070918},
KEYWORDS = {phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network}
}

4

Mihaela Baroni, Charles Semple and Mike Steel. A framework for representing reticulate evolution. In ACOM, Vol. 8:398-401, 2004.
Keywords: explicit network, from clusters, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction, regular network, SPR distance.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BSS04.pdf.

Toggle abstract

@Article{BSS2004,
AUTHOR = {Baroni, Mihaela and Semple, Charles and Steel, Mike},
TITLE = {A framework for representing reticulate evolution},
YEAR = {2004},
JOURNAL = {ACOM},
VOLUME = {8},
PAGES = {398-401},
URL = {http://dx.doi.org/10.1007/s00026-004-0228-0},
NOTE = {http://www.math.canterbury.ac.nz/~c.semple/papers/BSS04.pdf},
ANNOTE = {ISSUE : 4},
KEYWORDS = {explicit network, from clusters, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction, regular network, SPR distance}
}

5

Charles Choy, Jesper Jansson, Kunihiko Sadakane and Wing-Kin Sung. Computing the maximum agreement of phylogenetic networks. In Proceedings of Computing: the Tenth Australasian Theory Symposium (CATS'04), Vol. 91:134-147 of Electronic Notes in Theoretical Computer Science, 2004.
Keywords: dynamic programming, FPT, level k phylogenetic network, MASN, NP complete, phylogenetic network, phylogeny.
Note: http://www.df.lth.se/~jj/Publications/masn6_CATS2004.pdf.

Toggle abstract

@InProceedings{CJSS2004,
AUTHOR = {Choy, Charles and Jansson, Jesper and Sadakane, Kunihiko and Sung, Wing-Kin},
TITLE = {Computing the maximum agreement of phylogenetic networks},
YEAR = {2004},
BOOKTITLE = {Proceedings of Computing: the Tenth Australasian Theory Symposium (CATS'04)},
VOLUME = {91},
PAGES = {134-147},
SERIES = {Electronic Notes in Theoretical Computer Science},
URL = {http://dx.doi.org/10.1016/j.entcs.2003.12.009},
NOTE = {http://www.df.lth.se/~jj/Publications/masn6_CATS2004.pdf},
ANNOTE = {CITE : },
KEYWORDS = {dynamic programming, FPT, level k phylogenetic network, MASN, NP complete, phylogenetic network, phylogeny}
}

6

Tobias Dezulian and Mike Steel. Phylogenetic closure operations and homoplasy-free evolution. In IFCS04, Pages 395-416, springer, 2004.
Note: http://www.math.canterbury.ac.nz/~m.steel/Non_UC/files/research/closure_ops.pdf.

@InProceedings{DezulianSteel2004,
AUTHOR = {Dezulian, Tobias and Steel, Mike},
TITLE = {Phylogenetic closure operations and homoplasy-free evolution},
YEAR = {2004},
BOOKTITLE = {IFCS04},
PAGES = {395-416},
SERIES = {Classification, Clustering, and Data Mining Applications},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-642-17103-1_38},
NOTE = {http://www.math.canterbury.ac.nz/~m.steel/Non_UC/files/research/closure_ops.pdf},
ANNOTE = {CITE : }
}

7

Andreas W. M. Dress and Daniel H. Huson. Constructing splits graphs. In TCBB, Vol. 1(3):109-115, 2004.
Keywords: abstract network, circular split system, from trees, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network, visualization.
Note: http://scilib.kiev.ua/ieee/tcbb/2004/03/n3/n0109.pdf.

Toggle abstract

@Article{DressHuson2004,
AUTHOR = {Dress, Andreas W. M. and Huson, Daniel H.},
TITLE = {Constructing splits graphs},
YEAR = {2004},
JOURNAL = {TCBB},
VOLUME = {1},
NUMBER = {3},
PAGES = {109-115},
URL = {http://dx.doi.org/10.1109/TCBB.2004.27},
NOTE = {http://scilib.kiev.ua/ieee/tcbb/2004/03/n3/n0109.pdf},
ANNOTE = {CITE : },
KEYWORDS = {abstract network, circular split system, from trees, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network, visualization}
}

8

Dan Gusfield, Satish Eddhu and Charles Langley. Optimal, Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination. In JBCB, Vol. 2(1):173-213, 2004.
Keywords: explicit network, from sequences, galled tree, phylogenetic network, phylogeny, recombination, reconstruction.
Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/exfinalrec.pdf.

Toggle abstract

@Article{GEL2004b,
AUTHOR = {Gusfield, Dan and Eddhu, Satish and Langley, Charles},
TITLE = {Optimal, Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination},
YEAR = {2004},
JOURNAL = {JBCB},
VOLUME = {2},
NUMBER = {1},
PAGES = {173-213},
URL = {http://dx.doi.org/10.1142/S0219720004000521},
NOTE = {http://wwwcsif.cs.ucdavis.edu/~gusfield/exfinalrec.pdf},
ANNOTE = {CITE : },
KEYWORDS = {explicit network, from sequences, galled tree, phylogenetic network, phylogeny, recombination, reconstruction}
}

9

Dan Gusfield, Satish Eddhu and Charles Langley. The fine structure of galls in phylogenetic networks. In INCOMP, Vol. 16(4):459-469, 2004.
Keywords: explicit network, from sequences, galled tree, phylogenetic network, phylogeny, reconstruction.
Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/informs.pdf.

Toggle abstract

@Article{GEL2004,
AUTHOR = {Gusfield, Dan and Eddhu, Satish and Langley, Charles},
TITLE = {The fine structure of galls in phylogenetic networks},
YEAR = {2004},
JOURNAL = {INCOMP},
VOLUME = {16},
NUMBER = {4},
PAGES = {459-469},
URL = {http://dx.doi.org/10.1287/ijoc.1040.0099},
NOTE = {http://wwwcsif.cs.ucdavis.edu/~gusfield/informs.pdf},
ANNOTE = {CITE : },
KEYWORDS = {explicit network, from sequences, galled tree, phylogenetic network, phylogeny, reconstruction}
}

10

Dan Gusfield and Dean Hickerson. A Fundamental, Efficiently-Computed Lower Bound on the Number of Recombinations Needed in Phylogenetic Networks. 2004.
Note: UC Davis Computer Science Technical Report.

@Misc{GusfieldHickerson2004,
AUTHOR = {Gusfield, Dan and Hickerson, Dean},
TITLE = {A Fundamental, Efficiently-Computed Lower Bound on the Number of Recombinations Needed in Phylogenetic Networks},
YEAR = {2004},
NOTE = {UC Davis Computer Science Technical Report},
ANNOTE = {BIBUPDATE : 20070914}
}

11

Daniel H. Huson, Tobias Dezulian, Tobias Kloepper and Mike Steel. Phylogenetic Super-Networks from Partial Trees. In TCBB, Vol. 1(4):151-158, 2004.
Keywords: abstract network, from unrooted trees, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, supernetwork.
Note: http://hdl.handle.net/10092/3177.

Toggle abstract

@Article{HDKS2004,
AUTHOR = {Huson, Daniel H. and Dezulian, Tobias and Kloepper, Tobias and Steel, Mike},
TITLE = {Phylogenetic Super-Networks from Partial Trees},
YEAR = {2004},
JOURNAL = {TCBB},
VOLUME = {1},
NUMBER = {4},
PAGES = {151-158},
URL = {http://dx.doi.org/10.1109/TCBB.2004.44},
NOTE = {http://hdl.handle.net/10092/3177},
ANNOTE = {CITE : },
KEYWORDS = {abstract network, from unrooted trees, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, supernetwork}
}

12

Barbara R. Holland, Katharina Huber, Vincent Moulton and Peter J. Lockhart. Using consensus networks to visualize contradictory evidence for species phylogeny. In MBE, Vol. 21(7):1459-1461, 2004.
Keywords: consensus, from trees, phylogenetic network, phylogeny, split, visualization.
Note: http://dx.doi.org/10.1093/molbev/msh145.

Toggle abstract

@Article{HHML2004,
AUTHOR = {Holland, Barbara R. and Huber, Katharina and Moulton, Vincent and Lockhart, Peter J.},
TITLE = {Using consensus networks to visualize contradictory evidence for species phylogeny},
YEAR = {2004},
JOURNAL = {MBE},
VOLUME = {21},
NUMBER = {7},
PAGES = {1459-1461},
URL = {http://dx.doi.org/10.1093/molbev/msh145},
NOTE = {http://dx.doi.org/10.1093/molbev/msh145},
KEYWORDS = {consensus, from trees, phylogenetic network, phylogeny, split, visualization}
}

13

Katharina Huber, Michael Langton, David Penny, Vincent Moulton and Mike Hendy. Spectronet: A package for computing spectra and median networks. In ABIO, Vol. 1(3):159-161, 2004.
Keywords: from splits, median network, phylogenetic network, phylogeny, Program Spectronet, software, split, visualization.
Note: http://citeseer.ist.psu.edu/631776.html.

Toggle abstract

@Article{HLPM2002,
AUTHOR = {Huber, Katharina and Langton, Michael and Penny, David and Moulton, Vincent and Hendy, Mike},
TITLE = {Spectronet: A package for computing spectra and median networks},
YEAR = {2004},
JOURNAL = {ABIO},
VOLUME = {1},
NUMBER = {3},
PAGES = {159-161},
NOTE = {http://citeseer.ist.psu.edu/631776.html},
ANNOTE = {CITE : },
KEYWORDS = {from splits, median network, phylogenetic network, phylogeny, Program Spectronet, software, split, visualization}
}

14

Katharina Huber, Vincent Moulton and Charles Semple. Replacing cliques by stars in quasi-median graphs. In DAM, Vol. 143(1-3), 2004.
Note: http://dx.doi.org/10.1016/j.dam.2004.03.002.

Toggle abstract

@Article{HMS2004,
AUTHOR = {Huber, Katharina and Moulton, Vincent and Semple, Charles},
TITLE = {Replacing cliques by stars in quasi-median graphs},
YEAR = {2004},
JOURNAL = {DAM},
VOLUME = {143},
NUMBER = {1-3},
URL = {http://dx.doi.org/10.1016/j.dam.2004.03.002},
NOTE = {http://dx.doi.org/10.1016/j.dam.2004.03.002},
ANNOTE = {CITE : }
}

15

Jesper Jansson and Wing-Kin Sung. Inferring a level-1 phylogenetic network from a dense set of rooted triplets. In COCOON04, Vol. 3106:462-471 of LNCS, springer, 2004.
Keywords: explicit network, from triplets, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.df.lth.se/~jj/Publications/ipnrt6_COCOON2004.pdf.

@InProceedings{JanssonSung2004b,
AUTHOR = {Jansson, Jesper and Sung, Wing-Kin},
TITLE = {Inferring a level-1 phylogenetic network from a dense set of rooted triplets},
YEAR = {2004},
BOOKTITLE = {COCOON04},
VOLUME = {3106},
PAGES = {462-471},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-540-27798-9_49},
NOTE = {http://www.df.lth.se/~jj/Publications/ipnrt6_COCOON2004.pdf},
ANNOTE = {CITE : },
KEYWORDS = {explicit network, from triplets, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, polynomial, reconstruction}
}

16

C. Randal Linder and Loren H. Rieseberg. Reconstructing patterns of reticulate evolution in plants. In American Journal of Botany, Vol. 91(10):1700-1708, 2004.
Keywords: distance between networks, hybridization, phylogenetic network, phylogeny, reconstruction, survey, tripartition distance.
Note: http://www.amjbot.org/cgi/reprint/91/10/1700.pdf.

@Article{LinderRieseberg2004,
AUTHOR = {Linder, C. Randal and Rieseberg, Loren H.},
TITLE = {Reconstructing patterns of reticulate evolution in plants},
YEAR = {2004},
JOURNAL = {American Journal of Botany},
VOLUME = {91},
NUMBER = {10},
PAGES = {1700-1708},
URL = {http://dx.doi.org/10.3732/ajb.91.10.1700},
NOTE = {http://www.amjbot.org/cgi/reprint/91/10/1700.pdf},
ANNOTE = {BIBUPDATE : 20070904},
KEYWORDS = {distance between networks, hybridization, phylogenetic network, phylogeny, reconstruction, survey, tripartition distance}
}

17

Vladimir Makarenkov and Pierre Legendre. From a phylogenetic tree to a reticulated network. In JCB, Vol. 11(1):195-212, 2004.
Keywords: abstract network, from distances, phylogenetic network, phylogeny, Program T REX, reticulogram.
Note: http://www.labunix.uqam.ca/~makarenv/makarenv/article_JCB2004.pdf.

@Article{MakarenkovLegendre2004,
AUTHOR = {Makarenkov, Vladimir and Legendre, Pierre},
TITLE = {From a phylogenetic tree to a reticulated network},
YEAR = {2004},
JOURNAL = {JCB},
VOLUME = {11},
NUMBER = {1},
PAGES = {195-212},
URL = {http://dx.doi.org/10.1089/106652704773416966},
NOTE = {http://www.labunix.uqam.ca/~makarenv/makarenv/article_JCB2004.pdf},
ANNOTE = {BIBUPDATE : 20070918},
KEYWORDS = {abstract network, from distances, phylogenetic network, phylogeny, Program T REX, reticulogram}
}

18

Vladimir Makarenkov, Pierre Legendre and Yves Desdevises. Modeling phylogenetic relationships using reticulated networks. In Zoologica Scripta, Vol. 33(1):89-96, 2004.
Note: http://www.labunix.uqam.ca/~makarenv/articles/ZoologicaScripta.pdf.

@Article{MLD2004,
AUTHOR = {Makarenkov, Vladimir and Legendre, Pierre and Desdevises, Yves},
TITLE = {Modeling phylogenetic relationships using reticulated networks},
YEAR = {2004},
JOURNAL = {Zoologica Scripta},
VOLUME = {33},
NUMBER = {1},
PAGES = {89-96},
URL = {http://dx.doi.org/10.1111/j.1463-6409.2004.00141.x},
NOTE = {http://www.labunix.uqam.ca/~makarenv/articles/ZoologicaScripta.pdf},
ANNOTE = {BIBUPDATE : 20070918}
}

19

Bernard M. E. Moret, Luay Nakhleh, Tandy Warnow, C. Randal Linder, Anna Tholse, Anneke Padolina, Jerry Sun and Ruth Timme. Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy. In TCBB, Vol. 1(1):13-23, 2004.
Keywords: distance between networks, evaluation, phylogenetic network, phylogeny, time consistent network, tripartition distance.
Note: http://www.cs.rice.edu/~nakhleh/Papers/tcbb04.pdf.

@Article{MNWRTPST2004,
AUTHOR = {Moret, Bernard M. E. and Nakhleh, Luay and Warnow, Tandy and Linder, C. Randal and Tholse, Anna and Padolina, Anneke and Sun, Jerry and Timme, Ruth},
TITLE = {Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy},
YEAR = {2004},
JOURNAL = {TCBB},
VOLUME = {1},
NUMBER = {1},
PAGES = {13-23},
URL = {http://dx.doi.org/10.1109/tcbb.2004.10},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/tcbb04.pdf},
ANNOTE = {BIBUPDATE : 20070918},
KEYWORDS = {distance between networks, evaluation, phylogenetic network, phylogeny, time consistent network, tripartition distance}
}

20

Luay Nakhleh. Phylogenetic Networks. PhD thesis, University of Texas at Austin, U.S.A., 2004.
Keywords: distance between networks, evaluation, generation, phylogenetic network, phylogeny, Program SPNet, reconstruction, split, statistical model, tree sibling network.
Note: http://www.library.utexas.edu/etd/d/2004/nakhlehl042/nakhlehl042.pdf.

@PhdThesis{Nakhleh2004,
AUTHOR = {Nakhleh, Luay},
TITLE = {Phylogenetic Networks},
YEAR = {2004},
SCHOOL = {University of Texas at Austin, U.S.A.},
NOTE = {http://www.library.utexas.edu/etd/d/2004/nakhlehl042/nakhlehl042.pdf},
ANNOTE = {CITE : },
KEYWORDS = {distance between networks, evaluation, generation, phylogenetic network, phylogeny, Program SPNet, reconstruction, split, statistical model, tree sibling network}
}

21

Luay Nakhleh, Tandy Warnow and C. Randal Linder. Reconstructing reticulate evolution in species - theory and practice. In RECOMB04, Pages 337-346, 2004.
Keywords: from rooted trees, galled tree, phylogenetic network, phylogeny, polynomial, Program SPNet, reconstruction, software.
Note: http://www.cs.rice.edu/~nakhleh/Papers/144-nakhleh.pdf.

@InProceedings{NWL2004,
AUTHOR = {Nakhleh, Luay and Warnow, Tandy and Linder, C. Randal},
TITLE = {Reconstructing reticulate evolution in species - theory and practice},
YEAR = {2004},
BOOKTITLE = {RECOMB04},
PAGES = {337-346},
URL = {http://dx.doi.org/10.1145/974614.974659},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/144-nakhleh.pdf},
ANNOTE = {BIBUPDATE : 20070918},
KEYWORDS = {from rooted trees, galled tree, phylogenetic network, phylogeny, polynomial, Program SPNet, reconstruction, software}
}

22

Yun S. Song and Jotun Hein. On the Minimum Number of Recombination Events in the Evolutionary History of DNA Sequences. In JOMB, Vol. 48(2):160-186, 2004.
Keywords: minimum number, recombination.
Note: http://dx.doi.org/10.1007/s00285-003-0227-5.

Toggle abstract

@Article{SongHein2004,
AUTHOR = {Song, Yun S. and Hein, Jotun},
TITLE = {On the Minimum Number of Recombination Events in the Evolutionary History of DNA Sequences},
YEAR = {2004},
JOURNAL = {JOMB},
VOLUME = {48},
NUMBER = {2},
PAGES = {160-186},
URL = {http://dx.doi.org/10.1007/s00285-003-0227-5},
NOTE = {http://dx.doi.org/10.1007/s00285-003-0227-5},
ANNOTE = {CITE : },
KEYWORDS = {minimum number, recombination}
}

23

Mike Hallett, Jens Lagergren and Ali Tofigh. Simultaneous Identification of Duplications and Lateral Transfers. In RECOMB04, Pages 347-356, 2004.
Keywords: duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.nada.kth.se/~jensl/p164-hallett.pdf.

@InProceedings{HLT2004,
AUTHOR = {Hallett, Mike and Lagergren, Jens and Tofigh, Ali},
TITLE = {Simultaneous Identification of Duplications and Lateral Transfers},
YEAR = {2004},
BOOKTITLE = {RECOMB04},
PAGES = {347-356},
URL = {http://dx.doi.org/10.1145/974614.974660},
NOTE = {http://www.nada.kth.se/~jensl/p164-hallett.pdf},
ANNOTE = {CITE : },
KEYWORDS = {duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction}
}

24

Mike Hallett and Jens Lagergren. Efficient algorithms for lateral gene transfers problems. 2004.
Keywords: from rooted trees, lateral gene transfer, NP complete, phylogeny, polynomial, reconstruction.
Note: submitted to SIAM Journal on Computing, http://www.mcb.mcgill.ca/~hallett/Lateral.pdf.

@Misc{HallettLagergren2004,
AUTHOR = {Hallett, Mike and Lagergren, Jens},
TITLE = {Efficient algorithms for lateral gene transfers problems},
YEAR = {2004},
NOTE = {submitted to SIAM Journal on Computing, http://www.mcb.mcgill.ca/~hallett/Lateral.pdf},
ANNOTE = {CITE : },
KEYWORDS = {from rooted trees, lateral gene transfer, NP complete, phylogeny, polynomial, reconstruction}
}

25

C. Randal Linder, Bernard M. E. Moret, Luay Nakhleh and Tandy Warnow. Network (Reticulate) Evolution: Biology, Models, and Algorithms. In PSB04, 2004.
Note: http://www.cs.rice.edu/~nakhleh/Papers/psb04.pdf.

@InProceedings{LMNW2004,
AUTHOR = {Linder, C. Randal and Moret, Bernard M. E. and Nakhleh, Luay and Warnow, Tandy},
TITLE = {Network (Reticulate) Evolution: Biology, Models, and Algorithms},
YEAR = {2004},
BOOKTITLE = {PSB04},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/psb04.pdf},
ANNOTE = {BIBUPDATE : 20071121}
}

26

Mohd Abdul Hai Zahid, Ankush Mittal and Ramesh C. Joshi. Use of Phylogenetic network and its reconstruction Algorithms. In Bioinformatics India, Vol. 2:47-58, 2004.
Keywords: evaluation, from distances, NeighborNet, Program SplitsTree, Program T REX, split decomposition.
Note: http://www.isical.ac.in/~zahid_t/publications/papers/1.pdf.

@Article{ZMJ2004,
AUTHOR = {Zahid, Mohd Abdul Hai and Mittal, Ankush and Joshi, Ramesh C.},
TITLE = {Use of Phylogenetic network and its reconstruction Algorithms},
YEAR = {2004},
JOURNAL = {Bioinformatics India},
VOLUME = {2},
PAGES = {47-58},
NOTE = {http://www.isical.ac.in/~zahid_t/publications/papers/1.pdf},
ANNOTE = {ISSUE : 4},
KEYWORDS = {evaluation, from distances, NeighborNet, Program SplitsTree, Program T REX, split decomposition}
}

27

Pawel Górecki. Reconciliation problems for duplication, loss and horizontal gene transfer. In RECOMB04, Pages 316-325, 2004.
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://ai.stanford.edu/~serafim/CS374_2004/Papers/Gorecki_Reconciliation.pdf.

@InProceedings{Gorecki2004,
AUTHOR = {G{\~A}�recki, Pawel},
TITLE = {Reconciliation problems for duplication, loss and horizontal gene transfer},
YEAR = {2004},
BOOKTITLE = {RECOMB04},
PAGES = {316-325},
URL = {http://dx.doi.org/10.1145/974614.974656},
NOTE = {http://ai.stanford.edu/~serafim/CS374_2004/Papers/Gorecki_Reconciliation.pdf},
ANNOTE = {CITE : },
KEYWORDS = {duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction}
}

28

Alix Boc, Vladimir Makarenkov and Abdoulaye B. Diallo. Une nouvelle méthode pour la détection de transferts horizontaux de gène : la réconciliation topologique d'arbres de gène et d'espèces. In JOBIM04, 2004.
Note: http://www.labunix.uqam.ca/~makarenv/makarenv/JOBIM_2004.pdf.

@InProceedings{BMD2004,
AUTHOR = {Boc, Alix and Makarenkov, Vladimir and Diallo, Abdoulaye B.},
TITLE = {Une nouvelle m{\~A}�thode pour la d{\~A}�tection de transferts horizontaux de g{\~A}�ne : la r{\~A}�conciliation topologique d'arbres de g{\~A}�ne et d'esp{\~A}�ces},
YEAR = {2004},
BOOKTITLE = {JOBIM04},
NOTE = {http://www.labunix.uqam.ca/~makarenv/makarenv/JOBIM_2004.pdf}
}

29

Mihaela Baroni. Hybrid phylogenies : a graph-based approach to represent reticulate evolution. PhD thesis, University of Canterbury, New Zealand, 2004.
Keywords: explicit network, from rooted trees, galled tree, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction, regular network.
Note: http://ir.canterbury.ac.nz/bitstream/10092/4803/1/baroni_thesis.pdf.

@PhdThesis{Baroni2004,
AUTHOR = {Baroni, Mihaela},
TITLE = {Hybrid phylogenies : a graph-based approach to represent reticulate evolution},
YEAR = {2004},
SCHOOL = {University of Canterbury, New Zealand},
NOTE = {http://ir.canterbury.ac.nz/bitstream/10092/4803/1/baroni_thesis.pdf},
KEYWORDS = {explicit network, from rooted trees, galled tree, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction, regular network}
}

2003

1

Louigi Addario-Berry, Mike Hallett and Jens Lagergren. Towards Identifying Lateral Gene Transfer Events. In PSB03, 2003.
Keywords: evaluation, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, Program LatTrans, reconstruction.
Note: http://www.nada.kth.se/~jensl/AHLPsb.pdf.

@InProceedings{AHL2003,
AUTHOR = {Addario-Berry, Louigi and Hallett, Mike and Lagergren, Jens},
TITLE = {Towards Identifying Lateral Gene Transfer Events},
YEAR = {2003},
BOOKTITLE = {PSB03},
URL = {http://www.ncbi.nlm.nih.gov/pubmed/12603035},
NOTE = {http://www.nada.kth.se/~jensl/AHLPsb.pdf},
ANNOTE = {BIBUPDATE : 20070919},
KEYWORDS = {evaluation, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, Program LatTrans, reconstruction}
}

2

Alix Boc and Vladimir Makarenkov. New Efficient Algorithm for Detection of Horizontal Gene Transfer Events. In WABI03, Vol. 2812:190-201 of LNCS, springer, 2003.
Note: http://www.info2.uqam.ca/~makarenv/articles/article_WABI.pdf.

@InProceedings{BocMakarenkov2003,
AUTHOR = {Boc, Alix and Makarenkov, Vladimir},
TITLE = {New Efficient Algorithm for Detection of Horizontal Gene Transfer Events},
YEAR = {2003},
BOOKTITLE = {WABI03},
VOLUME = {2812},
PAGES = {190-201},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-540-39763-2_15},
NOTE = {http://www.info2.uqam.ca/~makarenv/articles/article_WABI.pdf},
ANNOTE = {BIBUPDATE : 20070918}
}

3

Dan Gusfield, Satish Eddhu and Charles Langley. Efficient reconstruction of phylogenetic networks with constrained recombination. In CSB03, Pages 363-374, 2003.
Keywords: explicit network, from sequences, galled tree, phylogenetic network, phylogeny, recombination, reconstruction.
Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/ieeefinal.pdf.

@InProceedings{GEL2003,
AUTHOR = {Gusfield, Dan and Eddhu, Satish and Langley, Charles},
TITLE = {Efficient reconstruction of phylogenetic networks with constrained recombination},
YEAR = {2003},
BOOKTITLE = {CSB03},
PAGES = {363-374},
URL = {http://dx.doi.org/10.1109/CSB.2003.1227337},
NOTE = {http://wwwcsif.cs.ucdavis.edu/~gusfield/ieeefinal.pdf},
ANNOTE = {CITE : },
KEYWORDS = {explicit network, from sequences, galled tree, phylogenetic network, phylogeny, recombination, reconstruction}
}

4

Barbara R. Holland and Vincent Moulton. Consensus networks: A method for visualising incompatibilities in collections of trees. In WABI03, Vol. 2812:165-176 of LNCS, springer, 2003.
Keywords: consensus.
Note: http://dx.doi.org/10.1093/molbev/msj061.

@InProceedings{HollandMoulton2003,
AUTHOR = {Holland, Barbara R. and Moulton, Vincent},
TITLE = {Consensus networks: A method for visualising incompatibilities in collections of trees},
YEAR = {2003},
BOOKTITLE = {WABI03},
VOLUME = {2812},
PAGES = {165-176},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1093/molbev/msj061},
NOTE = {http://dx.doi.org/10.1093/molbev/msj061},
ANNOTE = {BIBUPDATE : 20070920},
KEYWORDS = {consensus}
}

5

Simon R. Myers and Robert C. Griffiths. Bounds on the Minimum Number of Recombination Events in a Sample History. In GEN, Vol. 163:375-394, 2003.
Keywords: Program RecMin.
Note: http://www.genetics.org/cgi/content/abstract/163/1/375.

@Article{MyersGriffiths2003,
AUTHOR = {Myers, Simon R. and Griffiths, Robert C.},
TITLE = {Bounds on the Minimum Number of Recombination Events in a Sample History},
YEAR = {2003},
JOURNAL = {GEN},
VOLUME = {163},
PAGES = {375-394},
NOTE = {http://www.genetics.org/cgi/content/abstract/163/1/375},
ANNOTE = {CITE : },
KEYWORDS = {Program RecMin}
}

6

Luay Nakhleh, Jerry Sun, Tandy Warnow, C. Randal Linder, Bernard M. E. Moret and Anna Tholse. Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods. In PSB03, 2003.
Keywords: distance between networks, evaluation, phylogenetic network, phylogeny, polynomial, tripartition distance.
Note: http://www.cs.rice.edu/~nakhleh/Papers/psb03.pdf.

@InProceedings{NSWLMT2003,
AUTHOR = {Nakhleh, Luay and Sun, Jerry and Warnow, Tandy and Linder, C. Randal and Moret, Bernard M. E. and Tholse, Anna},
TITLE = {Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods},
YEAR = {2003},
BOOKTITLE = {PSB03},
URL = {http://dx.doi.org/10.1142/9789812776303_0030},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/psb03.pdf},
ANNOTE = {BIBUPDATE : 20070918},
KEYWORDS = {distance between networks, evaluation, phylogenetic network, phylogeny, polynomial, tripartition distance}
}

7

Yun S. Song and Jotun Hein. Parsimonious reconstruction of sequence evolution and haplotype blocks: Finding the minimum number of recombination events. In WABI03, Vol. 2812:287-302 of LNCS, springer, 2003.
Keywords: minimum number, recombination.
Note: http://www.cs.ucdavis.edu/~yssong/Pub/SH-WABI03.pdf.

@InProceedings{SongHein2003,
AUTHOR = {Song, Yun S. and Hein, Jotun},
TITLE = {Parsimonious reconstruction of sequence evolution and haplotype blocks: Finding the minimum number of recombination events},
YEAR = {2003},
BOOKTITLE = {WABI03},
VOLUME = {2812},
PAGES = {287-302},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-540-39763-2_22},
NOTE = {http://www.cs.ucdavis.edu/~yssong/Pub/SH-WABI03.pdf},
ANNOTE = {CITE : },
KEYWORDS = {minimum number, recombination}
}

8

Kirill Kryukov and Naruya Saitou. Netview: Application Software for Constructing and Visually Exploring Phylogenetic Networks. In Genome Informatics, Vol. 14:280-281, 2003.
Keywords: from sequences, phylogenetic network, phylogeny, Program NetView, visualization.
Note: http://www.jsbi.org/journal/GIW03/GIW03SS06.pdf.

@Article{KryukovSaitou2003,
AUTHOR = {Kryukov, Kirill and Saitou, Naruya},
TITLE = {Netview: Application Software for Constructing and Visually Exploring Phylogenetic Networks},
YEAR = {2003},
JOURNAL = {Genome Informatics},
VOLUME = {14},
PAGES = {280-281},
URL = {http://dx.doi.org/10.11234/gi1990.14.280},
NOTE = {http://www.jsbi.org/journal/GIW03/GIW03SS06.pdf},
ANNOTE = {CITE : },
KEYWORDS = {from sequences, phylogenetic network, phylogeny, Program NetView, visualization}
}

9

Esra Erdem, Vladimir Lifschitz, Luay Nakhleh and Don Ringe. Reconstructing the evolutionary history of Indo-European languages using answer set programming. In PADL03, Vol. 2562:160-176 of LNCS, springer, 2003.
Note: http://people.sabanciuniv.edu/~esraerdem/papers/padl03.ps.

@InProceedings{ELNR2003,
AUTHOR = {Erdem, Esra and Lifschitz, Vladimir and Nakhleh, Luay and Ringe, Don},
TITLE = {Reconstructing the evolutionary history of Indo-European languages using answer set programming},
YEAR = {2003},
BOOKTITLE = {PADL03},
VOLUME = {2562},
PAGES = {160-176},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/3-540-36388-2_12},
NOTE = {http://people.sabanciuniv.edu/~esraerdem/papers/padl03.ps}
}

10

Daniel H. Huson. What If I Don't Have a Tree? Split Decomposition and Related Models. In Current Protocols in Bioinformatics, Vol. Unit 6.7, 2003.
Keywords: abstract network, phylogenetic network, Program SplitsTree, software, split decomposition, split network.
Note: http://dx.doi.org/10.1002/0471250953.bi0607s01.

@Article{Huson2003,
AUTHOR = {Huson, Daniel H.},
TITLE = {What If I Don't Have a Tree? Split Decomposition and Related Models},
YEAR = {2003},
JOURNAL = {Current Protocols in Bioinformatics},
VOLUME = {Unit 6.7},
URL = {http://dx.doi.org/10.1002/0471250953.bi0607s01},
NOTE = {http://dx.doi.org/10.1002/0471250953.bi0607s01},
ANNOTE = {BIBUPDATE : 20081011},
KEYWORDS = {abstract network, phylogenetic network, Program SplitsTree, software, split decomposition, split network}
}

11

Pawel Górecki. Single step reconciliation algorithm for duplication, loss and horizontal gene transfer model. In ECCB03, 2003.
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.inra.fr/eccb2003/posters/pdf/short/S_gorecki.ps.

@InProceedings{Gorecki2003,
AUTHOR = {G{\~A}�recki, Pawel},
TITLE = {Single step reconciliation algorithm for duplication, loss and horizontal gene transfer model},
YEAR = {2003},
BOOKTITLE = {ECCB03},
NOTE = {http://www.inra.fr/eccb2003/posters/pdf/short/S_gorecki.ps},
ANNOTE = {BIBUPDATE : 20081127},
KEYWORDS = {duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction}
}

12

Vassily A. Lyubetsky and Vladimir V. V´yugin. Methods of horizontal gene transfer determination using phylogenetic data. In In Silico Biology, Vol. 3(1-2):17-31, 2003.
Note: http://www.bioinfo.de/isb/2003030003/.

@Article{LyubetskyVyugin2003,
AUTHOR = {Lyubetsky, Vassily A. and V{\^A}�yugin, Vladimir V.},
TITLE = {Methods of horizontal gene transfer determination using phylogenetic data},
YEAR = {2003},
JOURNAL = {In Silico Biology},
VOLUME = {3},
NUMBER = {1-2},
PAGES = {17-31},
NOTE = {http://www.bioinfo.de/isb/2003030003/},
ANNOTE = {BIBUPDATE : 20081127}
}

2002

1

David Bryant and Vincent Moulton. Neighbor-Net: An Agglomerative Method for the Construction of Planar Phylogenetic Networks. In WABI02, Vol. 2452:375-391 of LNCS, springer, 2002.
Keywords: abstract network, circular split system, from distances, NeighborNet, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network.
Note: http://dx.doi.org/10.1007/3-540-45784-4_28.

@InProceedings{BryantMoulton2002,
AUTHOR = {Bryant, David and Moulton, Vincent},
TITLE = {Neighbor-Net: An Agglomerative Method for the Construction of Planar Phylogenetic Networks},
YEAR = {2002},
BOOKTITLE = {WABI02},
VOLUME = {2452},
PAGES = {375-391},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/3-540-45784-4_28},
NOTE = {http://dx.doi.org/10.1007/3-540-45784-4_28},
ANNOTE = {CITE : },
KEYWORDS = {abstract network, circular split system, from distances, NeighborNet, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network}
}

2

Olivier Gauthier and François-Joseph Lapointe. A comparison of alternative methods for detecting reticulation events in phylogenetic analysis. In IFCS02, Pages 365-369, springer, 2002.

@InProceedings{GauthierLapointe2002,
AUTHOR = {Gauthier, Olivier and Lapointe, Fran{\~A}�ois-Joseph},
TITLE = {A comparison of alternative methods for detecting reticulation events in phylogenetic analysis},
YEAR = {2002},
BOOKTITLE = {IFCS02},
PAGES = {365-369},
SERIES = {Classification, Clustering and Data Analysis - Recent Advances and Applications},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-642-56181-8_37},
ANNOTE = {CITE : }
}

3

Dan Gusfield. Haplotyping as Perfect Phylogeny: Conceptual Framework and Efficient Solutions. In RECOMB02, 2002.
Keywords: haplotyping, perfect, phylogeny.
Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/acmhapre.pdf .

@InProceedings{Gusfield2002,
AUTHOR = {Gusfield, Dan},
TITLE = {Haplotyping as Perfect Phylogeny: Conceptual Framework and Efficient Solutions},
YEAR = {2002},
BOOKTITLE = {RECOMB02},
URL = {http://dx.doi.org/10.1145/565196.565218},
NOTE = {http://wwwcsif.cs.ucdavis.edu/~gusfield/acmhapre.pdf },
ANNOTE = {BIBUPDATE : 20070919},
KEYWORDS = {haplotyping, perfect, phylogeny}
}

4

Pierre Legendre and Vladimir Makarenkov. Reconstruction of biogeographic and evolutionary networks using reticulograms. In Systematic Biology, Vol. 51(2):199-216, 2002.
Keywords: phylogenetic network, phylogeny, reconstruction, reticulogram.
Note: http://www.labunix.uqam.ca/~makarenv/makarenv/Article_SB.pdf.

@Article{LegendreMakarenkov2002,
AUTHOR = {Legendre, Pierre and Makarenkov, Vladimir},
TITLE = {Reconstruction of biogeographic and evolutionary networks using reticulograms},
YEAR = {2002},
JOURNAL = {Systematic Biology},
VOLUME = {51},
NUMBER = {2},
PAGES = {199-216},
URL = {http://dx.doi.org/10.1080/10635150252899725},
NOTE = {http://www.labunix.uqam.ca/~makarenv/makarenv/Article_SB.pdf},
ANNOTE = {BIBUPDATE : 20070918},
KEYWORDS = {phylogenetic network, phylogeny, reconstruction, reticulogram}
}

5

Bernard M. E. Moret, Luay Nakhleh and Tandy Warnow. An error metric for phylogenetic networks. 2002.
Keywords: distance between networks, evaluation, phylogenetic network, phylogeny, tripartition distance.
Note: Technical report TR-02-09, http://www.cs.unm.edu/~treport/tr/03-05/nakhleh.ps.gz.

@Misc{MNW2002,
AUTHOR = {Moret, Bernard M. E. and Nakhleh, Luay and Warnow, Tandy},
TITLE = {An error metric for phylogenetic networks},
YEAR = {2002},
NOTE = {Technical report TR-02-09, http://www.cs.unm.edu/~treport/tr/03-05/nakhleh.ps.gz},
ANNOTE = {CITE : },
KEYWORDS = {distance between networks, evaluation, phylogenetic network, phylogeny, tripartition distance}
}

6

Luay Nakhleh, Don Ringe and Tandy Warnow. Perfect Phylogenetic Networks: A New Methodology for Reconstructing the Evolutionary History of Natural Languages. In Language, Journal of the Linguistic Society of America, Vol. 81(2):382-420, 2002.
Keywords: perfect, phylogenetic network, phylogeny.
Note: http://www.cs.rice.edu/~nakhleh/Papers/81.2nakhleh.pdf.

@Article{NRW2005b,
AUTHOR = {Nakhleh, Luay and Ringe, Don and Warnow, Tandy},
TITLE = {Perfect Phylogenetic Networks: A New Methodology for Reconstructing the Evolutionary History of Natural Languages},
YEAR = {2002},
JOURNAL = {Language, Journal of the Linguistic Society of America},
VOLUME = {81},
NUMBER = {2},
PAGES = {382-420},
URL = {http://dx.doi.org/10.1353/lan.2005.0078},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/81.2nakhleh.pdf},
ANNOTE = {CITE : },
KEYWORDS = {perfect, phylogenetic network, phylogeny}
}

7

David Posada, Keith A. Crandall and Edward C. Holmes. Recombination in Evolutionary Genomics. In ARG, Vol. 36:75-97, 2002.
Keywords: phylogenetic network, phylogeny, recombination, recombination detection, survey.
Note: http://dx.doi.org/10.1146/annurev.genet.36.040202.111115.

Toggle abstract

@Article{PCH2002,
AUTHOR = {Posada, David and Crandall, Keith A. and Holmes, Edward C.},
TITLE = {Recombination in Evolutionary Genomics},
YEAR = {2002},
JOURNAL = {ARG},
VOLUME = {36},
PAGES = {75-97},
URL = {http://dx.doi.org/10.1146/annurev.genet.36.040202.111115},
NOTE = {http://dx.doi.org/10.1146/annurev.genet.36.040202.111115},
ANNOTE = {BIBUPDATE : 20070927},
KEYWORDS = {phylogenetic network, phylogeny, recombination, recombination detection, survey}
}

8

David Posada and Keith A. Crandall. The effect of recombination on the accuracy of phylogeny estimation. In JME, Pages 396-402, 2002.
Note: http://darwin.uvigo.es/download/papers/17.recPhylo02.pdf.

@Article{PosadaCrandall2002,
AUTHOR = {Posada, David and Crandall, Keith A.},
TITLE = {The effect of recombination on the accuracy of phylogeny estimation},
YEAR = {2002},
JOURNAL = {JME},
PAGES = {396-402},
URL = {http://dx.doi.org/10.1007/s00239-001-0034-9},
NOTE = {http://darwin.uvigo.es/download/papers/17.recPhylo02.pdf},
ANNOTE = {BIBUPDATE : 20070919}
}

2001

1

Mike Hallett and Jens Lagergren. Efficient algorithms for lateral gene transfers problems. In RECOMB01, Pages 141-148, 2001.
Keywords: from rooted trees, lateral gene transfer, NP complete, phylogeny, polynomial, Program McKiTscH, reconstruction.
Note: http://dx.doi.org/10.1145/369133.369188.

@InProceedings{HallettLagergren2001,
AUTHOR = {Hallett, Mike and Lagergren, Jens},
TITLE = {Efficient algorithms for lateral gene transfers problems},
YEAR = {2001},
BOOKTITLE = {RECOMB01},
PAGES = {141-148},
URL = {http://dx.doi.org/10.1145/369133.369188},
NOTE = {http://dx.doi.org/10.1145/369133.369188},
ANNOTE = {CITE : },
KEYWORDS = {from rooted trees, lateral gene transfer, NP complete, phylogeny, polynomial, Program McKiTscH, reconstruction}
}

2

Katharina Huber, Vincent Moulton, Peter J. Lockhart and Andreas W. M. Dress. Pruned Median Networks: A Technique for Reducing the Complexity of Median Networks. In MPE, Vol. 19(2):302-310, 2001.
Keywords: abstract network, median network, phylogenetic network, phylogeny, split.
Note: http://dx.doi.org/10.1006/mpev.2001.0935.

Toggle abstract

@Article{HMPD2001,
AUTHOR = {Huber, Katharina and Moulton, Vincent and Lockhart, Peter J. and Dress, Andreas W. M.},
TITLE = {Pruned Median Networks: A Technique for Reducing the Complexity of Median Networks},
YEAR = {2001},
JOURNAL = {MPE},
VOLUME = {19},
NUMBER = {2},
PAGES = {302-310},
URL = {http://dx.doi.org/10.1006/mpev.2001.0935},
NOTE = {http://dx.doi.org/10.1006/mpev.2001.0935},
ANNOTE = {CITE : },
KEYWORDS = {abstract network, median network, phylogenetic network, phylogeny, split}
}

3

Barbara R. Holland. Evolutionary analyses of large data sets: Trees and beyond. PhD thesis, Massey University, New Zealand, 2001.
Keywords: median network, split.
Note: http://mro.massey.ac.nz/handle/10179/2078.

@PhdThesis{Holland2001,
AUTHOR = {Holland, Barbara R.},
TITLE = {Evolutionary analyses of large data sets: Trees and beyond},
YEAR = {2001},
SCHOOL = {Massey University, New Zealand},
NOTE = {http://mro.massey.ac.nz/handle/10179/2078},
ANNOTE = {CITE : },
KEYWORDS = {median network, split}
}

4

Vladimir Makarenkov. T-REX: reconstructing and visualizing phylogenetic trees and reticulation networks. In BIO, Vol. 17(7):664-668, 2001.
Keywords: phylogenetic network, phylogeny, Program T REX, reconstruction, reticulogram, software, visualization.
Note: http://www.labunix.uqam.ca/~makarenv/makarenv/Article_BIO.pdf.

@Article{Makarenkov2001,
AUTHOR = {Makarenkov, Vladimir},
TITLE = {T-REX: reconstructing and visualizing phylogenetic trees and reticulation networks},
YEAR = {2001},
JOURNAL = {BIO},
VOLUME = {17},
NUMBER = {7},
PAGES = {664-668},
URL = {http://dx.doi.org/10.1093/bioinformatics/17.7.664},
NOTE = {http://www.labunix.uqam.ca/~makarenv/makarenv/Article_BIO.pdf},
ANNOTE = {BIBUPDATE : 20070918},
KEYWORDS = {phylogenetic network, phylogeny, Program T REX, reconstruction, reticulogram, software, visualization}
}

5

David Posada and Keith A. Crandall. Intraspecific gene genealogies: trees grafting into networks. In TEE, Vol. 16(1):37-45, 2001.
Keywords: likelihood, median network, netting, parsimony, phylogenetic network, phylogeny, Program Arlequin, Program SplitsTree, Program T REX, Program TCS, pyramid, reticulogram, split decomposition, statistical parsimony, survey.
Note: http://darwin.uvigo.es/download/papers/09.networks01.pdf.

@Article{PosadaCrandall2001,
AUTHOR = {Posada, David and Crandall, Keith A.},
TITLE = {Intraspecific gene genealogies: trees grafting into networks},
YEAR = {2001},
JOURNAL = {TEE},
VOLUME = {16},
NUMBER = {1},
PAGES = {37-45},
URL = {http://dx.doi.org/10.1016/s0169-5347(00)02026-7},
NOTE = {http://darwin.uvigo.es/download/papers/09.networks01.pdf},
ANNOTE = {BIBUPDATE : 20070917},
KEYWORDS = {likelihood, median network, netting, parsimony, phylogenetic network, phylogeny, Program Arlequin, Program SplitsTree, Program T REX, Program TCS, pyramid, reticulogram, split decomposition, statistical parsimony, survey}
}

6

Korbinian Strimmer, Carsten Wiuf and Vincent Moulton. Recombination Analysis Using Directed Graphical Models. In MBE, Vol. 18(1):97-99, 2001.
Keywords: recombination, statistical model.
Note: http://mbe.oxfordjournals.org/cgi/content/full/18/1/97.

@Article{SWM2001,
AUTHOR = {Strimmer, Korbinian and Wiuf, Carsten and Moulton, Vincent},
TITLE = {Recombination Analysis Using Directed Graphical Models},
YEAR = {2001},
JOURNAL = {MBE},
VOLUME = {18},
NUMBER = {1},
PAGES = {97-99},
URL = {http://dx.doi.org/10.1093/oxfordjournals.molbev.a003725},
NOTE = {http://mbe.oxfordjournals.org/cgi/content/full/18/1/97},
ANNOTE = {BIBUPDATE : 20070918},
KEYWORDS = {recombination, statistical model}
}

7

Lusheng Wang, Kaizhong Zhang and Louxin Zhang. Perfect phylogenetic networks with recombination. In SAC01, Pages 46-50, 2001.
Keywords: from sequences, galled tree, NP complete, perfect, phylogenetic network, phylogeny, polynomial, recombination, reconstruction.
Note: http://dx.doi.org/10.1145/372202.372271.

@InProceedings{WZZ2001,
AUTHOR = {Wang, Lusheng and Zhang, Kaizhong and Zhang, Louxin},
TITLE = {Perfect phylogenetic networks with recombination},
YEAR = {2001},
BOOKTITLE = {SAC01},
PAGES = {46-50},
URL = {http://dx.doi.org/10.1145/372202.372271},
NOTE = {http://dx.doi.org/10.1145/372202.372271},
ANNOTE = {CITE : },
KEYWORDS = {from sequences, galled tree, NP complete, perfect, phylogenetic network, phylogeny, polynomial, recombination, reconstruction}
}

8

Andreas W. M. Dress, Katharina Huber and Vincent Moulton. Hereditarily Optimal Realizations: Why are they Relevant in Phylogenetic Analysis, and how does one Compute them? In Proceedings of the Euroconference on Algebraic Combinatorics and Applications (Alcoma'99), Pages 110-117, springer, 2001.
Keywords: abstract network, from distances, optimal realization, phylogenetic network.
Note: http://www.math.uni-bielefeld.de/fsp-math/Preprints/139.pdf.

@InProceedings{DHM2001,
AUTHOR = {Dress, Andreas W. M. and Huber, Katharina and Moulton, Vincent},
TITLE = {Hereditarily Optimal Realizations: Why are they Relevant in Phylogenetic Analysis, and how does one Compute them?},
YEAR = {2001},
BOOKTITLE = {Proceedings of the Euroconference on Algebraic Combinatorics and Applications (Alcoma'99)},
PAGES = {110-117},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-642-59448-9_8},
NOTE = {http://www.math.uni-bielefeld.de/fsp-math/Preprints/139.pdf},
ANNOTE = {BIBUPDATE : 20080513},
KEYWORDS = {abstract network, from distances, optimal realization, phylogenetic network}
}

9

Mark T. Holder, Jennifer A. Anderson and Alisha K. Holloway. Difficulties in Detecting Hybridization. In Systematic Biology, Vol. 50(6):978-982, 2001.
Keywords: bootstrap, from rooted trees, hybridization, lateral gene transfer, lineage sorting, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: http://dx.doi.org/10.1080/106351501753462911.

Toggle abstract [No abstract available]

@Article{HAH2001,
AUTHOR = {Holder, Mark T. and Anderson, Jennifer A. and Holloway, Alisha K.},
TITLE = {Difficulties in Detecting Hybridization},
YEAR = {2001},
JOURNAL = {Systematic Biology},
VOLUME = {50},
NUMBER = {6},
PAGES = {978-982},
URL = {http://dx.doi.org/10.1080/106351501753462911},
NOTE = {http://dx.doi.org/10.1080/106351501753462911},
KEYWORDS = {bootstrap, from rooted trees, hybridization, lateral gene transfer, lineage sorting, phylogenetic network, phylogeny, reconstruction, statistical model}
}

10

Walter M. Fitch. Reticulation. In Sydney Brenner and Jeffrey H. Miller editors, Encyclopedia of Genetics, Academic Press, 2001.
Keywords: phylogenetic network, phylogeny, survey.

@InBook{Fitch2001,
AUTHOR = {Fitch, Walter M.},
TITLE = {Reticulation},
YEAR = {2001},
BOOKTITLE = {Encyclopedia of Genetics},
EDITOR = {Brenner, Sydney and Miller, Jeffrey H.},
PUBLISHER = {Academic Press},
URL = {http://dx.doi.org/10.1006/rwgn.2001.1486},
KEYWORDS = {phylogenetic network, phylogeny, survey}
}

2000

1

Hans-Jürgen Bandelt, Vincent Macaulay and Martin Richards. Median networks: speedy construction and greedy reduction, one simulation, and two case studies from human mtDNA. In MPE, Vol. 16:8-28, 2000.
Keywords: from sequences, from splits, median network, phylogenetic network, phylogeny, reconstruction.
Note: http://www.stats.gla.ac.uk/~vincent/papers/speedy.pdf.

Toggle abstract

@Article{BMR2000,
AUTHOR = {Bandelt, Hans-J{\~A}�rgen and Macaulay, Vincent and Richards, Martin},
TITLE = {Median networks: speedy construction and greedy reduction, one simulation, and two case studies from human mtDNA},
YEAR = {2000},
JOURNAL = {MPE},
VOLUME = {16},
PAGES = {8-28},
URL = {http://dx.doi.org/10.1006/mpev.2000.0792},
NOTE = {http://www.stats.gla.ac.uk/~vincent/papers/speedy.pdf},
ANNOTE = {CITE : },
KEYWORDS = {from sequences, from splits, median network, phylogenetic network, phylogeny, reconstruction}
}

2

Mark Clement, David Posada and Keith A. Crandall. TCS: a computer program to estimate gene genealogies. In MOLE, Vol. 9:1657-1659, 2000.
Keywords: from sequences, parsimony, phylogenetic network, phylogeny, Program TCS, reconstruction, software, statistical parsimony.
Note: http://darwin.uvigo.es/download/papers/08.tcs00.pdf.

Toggle abstract [No abstract available]

@Article{CPC2000,
AUTHOR = {Clement, Mark and Posada, David and Crandall, Keith A.},
TITLE = {TCS: a computer program to estimate gene genealogies},
YEAR = {2000},
JOURNAL = {MOLE},
VOLUME = {9},
PAGES = {1657-1659},
URL = {http://dx.doi.org/10.1046/j.1365-294x.2000.01020.x},
NOTE = {http://darwin.uvigo.es/download/papers/08.tcs00.pdf},
KEYWORDS = {from sequences, parsimony, phylogenetic network, phylogeny, Program TCS, reconstruction, software, statistical parsimony}
}

3

François-Joseph Lapointe. How to account for reticulation events in phylogenetic analysis: A review of distance-based methods. In Journal of Classification, Vol. 17:175-184, 2000.
Keywords: abstract network, evaluation, from distances, phylogenetic network, Program Pyramids, Program SplitsTree, Program T REX, pyramid, reconstruction, reticulogram, split network, survey, weak hierarchy.
Note: http://dx.doi.org/10.1007/s003570000016.

@Article{Lapointe2000,
AUTHOR = {Lapointe, Fran{\~A}�ois-Joseph},
TITLE = {How to account for reticulation events in phylogenetic analysis: A review of distance-based methods},
YEAR = {2000},
JOURNAL = {Journal of Classification},
VOLUME = {17},
PAGES = {175-184},
URL = {http://dx.doi.org/10.1007/s003570000016},
NOTE = {http://dx.doi.org/10.1007/s003570000016},
ANNOTE = {CITE : },
KEYWORDS = {abstract network, evaluation, from distances, phylogenetic network, Program Pyramids, Program SplitsTree, Program T REX, pyramid, reconstruction, reticulogram, split network, survey, weak hierarchy}
}

4

Pierre Legendre. Reticulate evolution: From bacteria to philosophers. In JCLA, Vol. 17:153-157, 2000.
Note: http://www.bio.umontreal.ca/legendre/reprints/Special_Section.pdf.

@Article{Legendre2000a,
AUTHOR = {Legendre, Pierre},
TITLE = {Reticulate evolution: From bacteria to philosophers},
YEAR = {2000},
JOURNAL = {JCLA},
VOLUME = {17},
PAGES = {153-157},
URL = {http://dx.doi.org/10.1007/s003570000013},
NOTE = {http://www.bio.umontreal.ca/legendre/reprints/Special_Section.pdf},
ANNOTE = {BIBUPDATE : 20070918}
}

5

Pierre Legendre. Biological Applications of Reticulate Analysis. In JCLA, Vol. 17:191-195, 2000.
Note: http://www.bio.umontreal.ca/legendre/reprints/Special_Section.pdf.

@Article{Legendre2000b,
AUTHOR = {Legendre, Pierre},
TITLE = {Biological Applications of Reticulate Analysis},
YEAR = {2000},
JOURNAL = {JCLA},
VOLUME = {17},
PAGES = {191-195},
URL = {http://dx.doi.org/10.1007/s003570000018},
NOTE = {http://www.bio.umontreal.ca/legendre/reprints/Special_Section.pdf},
ANNOTE = {BIBUPDATE : 20070918}
}

6

F. James Rohlf. Phylogenetic models and reticulations. In JCLA, Vol. 17:185-189, 2000.
Note: http://www.bio.umontreal.ca/legendre/reprints/Special_Section.pdf.

@Article{Rohlf2000,
AUTHOR = {Rohlf, F. James},
TITLE = {Phylogenetic models and reticulations},
YEAR = {2000},
JOURNAL = {JCLA},
VOLUME = {17},
PAGES = {185-189},
URL = {http://dx.doi.org/10.1007/s003570000017},
NOTE = {http://www.bio.umontreal.ca/legendre/reprints/Special_Section.pdf},
ANNOTE = {BIBUPDATE : 20070918}
}

7

Mikkel H. Schierup and Jotun Hein. Consequences of recombination on traditional phylogenetic analysis. In GEN, Vol. 156:879-891, 2000.
Note: http://www.birc.dk/Publications/Articles/Schierup_2000b.pdf.

@Article{SchierupHein2000a,
AUTHOR = {Schierup, Mikkel H. and Hein, Jotun},
TITLE = {Consequences of recombination on traditional phylogenetic analysis},
YEAR = {2000},
JOURNAL = {GEN},
VOLUME = {156},
PAGES = {879-891},
NOTE = {http://www.birc.dk/Publications/Articles/Schierup_2000b.pdf},
ANNOTE = {BIBUPDATE : 20070917}
}

8

Mikkel H. Schierup and Jotun Hein. Recombination and the molecular clock. In MBE, Vol. 17(10):1578-1579, 2000.
Note: http://www.birc.dk/Publications/Articles/Schierup_2000c.pdf.

@Article{SchierupHein2000b,
AUTHOR = {Schierup, Mikkel H. and Hein, Jotun},
TITLE = {Recombination and the molecular clock},
YEAR = {2000},
JOURNAL = {MBE},
VOLUME = {17},
NUMBER = {10},
PAGES = {1578-1579},
URL = {http://dx.doi.org/10.1093/oxfordjournals.molbev.a026256},
NOTE = {http://www.birc.dk/Publications/Articles/Schierup_2000c.pdf},
ANNOTE = {BIBUPDATE : 20070917}
}

9

Peter E. Smouse. Reticulation inside the species boundary. In JCLA, Vol. 17:165-173, 2000.
Note: http://www.bio.umontreal.ca/legendre/reprints/Special_Section.pdf.

@Article{Smouse2000,
AUTHOR = {Smouse, Peter E.},
TITLE = {Reticulation inside the species boundary},
YEAR = {2000},
JOURNAL = {JCLA},
VOLUME = {17},
PAGES = {165-173},
URL = {http://dx.doi.org/10.1007/s003570000015},
NOTE = {http://www.bio.umontreal.ca/legendre/reprints/Special_Section.pdf},
ANNOTE = {BIBUPDATE : 20070918}
}

10

Peter H. A. Sneath. Reticulate Evolution in Bacteria and Other Organisms: How Can We Study It? In JCLA, Vol. 17:360-368, 2000.
Note: http://www.bio.umontreal.ca/legendre/reprints/Special_Section.pdf.

@Article{Sneath2000,
AUTHOR = {Sneath, Peter H. A.},
TITLE = {Reticulate Evolution in Bacteria and Other Organisms: How Can We Study It?},
YEAR = {2000},
JOURNAL = {JCLA},
VOLUME = {17},
PAGES = {360-368},
URL = {http://dx.doi.org/10.1007/s003570000014},
NOTE = {http://www.bio.umontreal.ca/legendre/reprints/Special_Section.pdf},
ANNOTE = {BIBUPDATE : 20070918}
}

11

Korbinian Strimmer and Vincent Moulton. Likelihood Analysis of Phylogenetic Networks Using Directed Graphical Models. In MBE, Vol. 17(6):875-881, 2000.
Keywords: bayesian, likelihood, median network, split network, statistical model.
Note: http://mbe.oxfordjournals.org/cgi/content/abstract/17/6/875.

@Article{StrimmerMoulton2000,
AUTHOR = {Strimmer, Korbinian and Moulton, Vincent},
TITLE = {Likelihood Analysis of Phylogenetic Networks Using Directed Graphical Models},
YEAR = {2000},
JOURNAL = {MBE},
VOLUME = {17},
NUMBER = {6},
PAGES = {875-881},
URL = {http://dx.doi.org/10.1093/oxfordjournals.molbev.a026367},
NOTE = {http://mbe.oxfordjournals.org/cgi/content/abstract/17/6/875},
ANNOTE = {BIBUPDATE : 20070917},
KEYWORDS = {bayesian, likelihood, median network, split network, statistical model}
}

12

Alan R. Templeton, Keith A. Crandall and Charles F. Sing. A Cladistic Analysis of Phenotypic Associations With Haplotypes Inferred From Restriction Endonuclease Mapping and DNA Sequence Data. III. Cladogram Estimation. In GEN, Vol. 132:619-633, 2000.
Keywords: from sequences, parsimony, phylogenetic network, phylogeny, Program TCS, recombination, reconstruction, statistical parsimony.
Note: http://www.genetics.org/cgi/content/abstract/132/2/619.

@Article{TCS1992,
AUTHOR = {Templeton, Alan R. and Crandall, Keith A. and Sing, Charles F.},
TITLE = {A Cladistic Analysis of Phenotypic Associations With Haplotypes Inferred From Restriction Endonuclease Mapping and DNA Sequence Data. III. Cladogram Estimation},
YEAR = {2000},
JOURNAL = {GEN},
VOLUME = {132},
PAGES = {619-633},
NOTE = {http://www.genetics.org/cgi/content/abstract/132/2/619},
ANNOTE = {CITE : },
KEYWORDS = {from sequences, parsimony, phylogenetic network, phylogeny, Program TCS, recombination, reconstruction, statistical parsimony}
}

13

Shizhong Xu. Phylogenetic Analysis Under Reticulate Evolution. In MBE, Vol. 17(6):897-907, 2000.
Keywords: from distances, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: http://mbe.oxfordjournals.org/cgi/content/abstract/17/6/897.

@Article{Xu2000,
AUTHOR = {Xu, Shizhong},
TITLE = {Phylogenetic Analysis Under Reticulate Evolution},
YEAR = {2000},
JOURNAL = {MBE},
VOLUME = {17},
NUMBER = {6},
PAGES = {897-907},
URL = {http://dx.doi.org/10.1093/oxfordjournals.molbev.a026370},
NOTE = {http://mbe.oxfordjournals.org/cgi/content/abstract/17/6/897},
ANNOTE = {BIBUPDATE : 20070918},
KEYWORDS = {from distances, phylogenetic network, phylogeny, reconstruction, statistical model}
}

14

Katharina Huber, Elizabeth E. Watson and Mike Hendy. An Algorithm for Constructing Local Regions in a Phylogenetic Network. In MPE, Vol. 19(1):1-8, 2000.
Keywords: abstract network, median network, phylogenetic network, phylogeny, reconstruction, split.
Note: http://dx.doi.org/10.1006/mpev.2000.0891.

Toggle abstract

@Article{HWH2001,
AUTHOR = {Huber, Katharina and Watson, Elizabeth E. and Hendy, Mike},
TITLE = {An Algorithm for Constructing Local Regions in a Phylogenetic Network},
YEAR = {2000},
JOURNAL = {MPE},
VOLUME = {19},
NUMBER = {1},
PAGES = {1-8},
URL = {http://dx.doi.org/10.1006/mpev.2000.0891},
NOTE = {http://dx.doi.org/10.1006/mpev.2000.0891},
ANNOTE = {BIBUPDATE : 20071122},
KEYWORDS = {abstract network, median network, phylogenetic network, phylogeny, reconstruction, split}
}

15

Pierre Legendre and Vladimir Makarenkov. Improving the additive tree representation of a dissimilarity matrix using reticulations. In IFCS00, Pages 35-40, springer, 2000.
Keywords: phylogenetic network, phylogeny, reconstruction, reticulogram.
Note: http://www.info2.uqam.ca/~makarenv/makarenv/Article_IFCS.pdf.

@InProceedings{LegendreMakarenkov2000,
AUTHOR = {Legendre, Pierre and Makarenkov, Vladimir},
TITLE = {Improving the additive tree representation of a dissimilarity matrix using reticulations},
YEAR = {2000},
BOOKTITLE = {IFCS00},
PAGES = {35-40},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-642-59789-3_5},
NOTE = {http://www.info2.uqam.ca/~makarenv/makarenv/Article_IFCS.pdf},
ANNOTE = {BIBUPDATE : 20080616},
KEYWORDS = {phylogenetic network, phylogeny, reconstruction, reticulogram}
}

16

Bin Ma, Lusheng Wang and Ming Li. Fixed topology alignment with recombination. In DAM, Vol. 104:281-300, 2000.
Keywords: approximation, explicit network, from network, from sequences, galled tree, inapproximability, phylogenetic network, phylogeny, recombination.
Note: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.40.7759.

Toggle abstract

@Article{MWL2000,
AUTHOR = {Ma, Bin and Wang, Lusheng and Li, Ming},
TITLE = {Fixed topology alignment with recombination},
YEAR = {2000},
JOURNAL = {DAM},
VOLUME = {104},
PAGES = {281-300},
URL = {http://dx.doi.org/10.1186/1471-2105-15-127},
NOTE = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.40.7759},
ANNOTE = {BIBUPDATE : 20081225},
KEYWORDS = {approximation, explicit network, from network, from sequences, galled tree, inapproximability, phylogenetic network, phylogeny, recombination}
}

17

Tao Sang and Yang Zhong. Testing Hybridization Hypotheses Based on Incongruent Gene Trees. In Systematic Biology, Vol. 49(3):422-434, 2000.
Keywords: bootstrap, from rooted trees, hybridization, lateral gene transfer, lineage sorting, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: http://dx.doi.org/10.1080/10635159950127321.

@Article{SangZhong2010,
AUTHOR = {Sang, Tao and Zhong, Yang},
TITLE = {Testing Hybridization Hypotheses Based on Incongruent Gene Trees},
YEAR = {2000},
JOURNAL = {Systematic Biology},
VOLUME = {49},
NUMBER = {3},
PAGES = {422-434},
URL = {http://dx.doi.org/10.1080/10635159950127321},
NOTE = {http://dx.doi.org/10.1080/10635159950127321},
KEYWORDS = {bootstrap, from rooted trees, hybridization, lateral gene transfer, lineage sorting, phylogenetic network, phylogeny, reconstruction, statistical model}
}

1999

1

Jean-Christophe Aude, Yolande Diaz-Lazcoz, Jean-Jacques Codani and Jean-Loup Risler. Applications of the Pyramidal Clustering Method to Biological Objects. In CC, Vol. 23(3-4):303-315, 1999.
Keywords: from distances, phylogenetic network, phylogeny, Program Pyramids, pyramid, reconstruction, software, visualization.
Note: http://dx.doi.org/10.1016/S0097-8485(99)00006-6.

@Article{ADCR1999,
AUTHOR = {Aude, Jean-Christophe and Diaz-Lazcoz, Yolande and Codani, Jean-Jacques and Risler, Jean-Loup},
TITLE = {Applications of the Pyramidal Clustering Method to Biological Objects},
YEAR = {1999},
JOURNAL = {CC},
VOLUME = {23},
NUMBER = {3-4},
PAGES = {303-315},
URL = {http://dx.doi.org/10.1016/S0097-8485(99)00006-6},
NOTE = {http://dx.doi.org/10.1016/S0097-8485(99)00006-6},
ANNOTE = {CITE : },
KEYWORDS = {from distances, phylogenetic network, phylogeny, Program Pyramids, pyramid, reconstruction, software, visualization}
}

2

Hans-Jürgen Bandelt, Peter Forster and Arne Röhl. Median-joining networks for inferring intraspecies phylogenies. In MBE, Vol. 16(1):37-48, 1999.
Keywords: from sequences, median network, MedianJoining, Program Network, reconstruction, software.
Note: http://mbe.oxfordjournals.org/cgi/content/abstract/16/1/37.

@Article{BFR1999,
AUTHOR = {Bandelt, Hans-J{\~A}�rgen and Forster, Peter and R{\~A}�hl, Arne},
TITLE = {Median-joining networks for inferring intraspecies phylogenies},
YEAR = {1999},
JOURNAL = {MBE},
VOLUME = {16},
NUMBER = {1},
PAGES = {37-48},
URL = {http://www.ncbi.nlm.nih.gov/pubmed/10331250},
NOTE = {http://mbe.oxfordjournals.org/cgi/content/abstract/16/1/37},
ANNOTE = {BIBUPDATE : 20070918},
KEYWORDS = {from sequences, median network, MedianJoining, Program Network, reconstruction, software}
}

3

W. Ford Doolittle. Phylogenetic Classification and the Universal Tree. In Science, Vol. 284:2124-2128, 1999.
Note: http://cas.bellarmine.edu/tietjen/Ecology/phylogenetic_classification_and_.htm.

Toggle abstract

@Article{Doolittle1999,
AUTHOR = {Doolittle, W. Ford},
TITLE = {Phylogenetic Classification and the Universal Tree},
YEAR = {1999},
JOURNAL = {Science},
VOLUME = {284},
PAGES = {2124-2128},
URL = {http://dx.doi.org/10.1126/science.284.5423.2124},
NOTE = {http://cas.bellarmine.edu/tietjen/Ecology/phylogenetic_classification_and_.htm},
ANNOTE = {CITE : }
}

4

Arne Röhl. Phylogenetische Netzwerke. PhD thesis, Universität Hamburg, Germany, 1999.
Note: http://www.sub.uni-hamburg.de/opus/volltexte/1999/53/html/Phylogenetische_Netzwerke.html.

@PhdThesis{Rohl1999,
AUTHOR = {R{\~A}�hl, Arne},
TITLE = {Phylogenetische Netzwerke},
YEAR = {1999},
SCHOOL = {Universit{\~A}�t Hamburg, Germany},
NOTE = {http://www.sub.uni-hamburg.de/opus/volltexte/1999/53/html/Phylogenetische_Netzwerke.html},
ANNOTE = {BIBUPDATE : 20070918}
}

5

Nicholas C. Grassly and Andrew Rambaut. Treevolve, a program to simulate the evolution of DNA sequences under different population dynamic scenarios. 1999.
Keywords: generation, phylogenetic network, phylogeny, population genetics, Program Treevolve, software.
Note: http://evolve.zoo.ox.ac.uk/software/treevolve/manual.php.

@Misc{GrasslyRambaut1999,
AUTHOR = {Grassly, Nicholas C. and Rambaut, Andrew},
TITLE = {Treevolve, a program to simulate the evolution of DNA sequences under different population dynamic scenarios},
YEAR = {1999},
NOTE = {http://evolve.zoo.ox.ac.uk/software/treevolve/manual.php},
ANNOTE = {BIBUPDATE : 20071228},
KEYWORDS = {generation, phylogenetic network, phylogeny, population genetics, Program Treevolve, software}
}

6

Vincent Berry and David Bryant. Faster reliable phylogenetic analysis. In RECOMB99, Pages 59-68, 1999.
Keywords: abstract network, from quartets, phylogenetic network, phylogeny, polynomial, Program SplitsTree, reconstruction, split network, weakly compatible.
Note: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.95.9151.

@InProceedings{BerryBryant1999,
AUTHOR = {Berry, Vincent and Bryant, David},
TITLE = {Faster reliable phylogenetic analysis},
YEAR = {1999},
BOOKTITLE = {RECOMB99},
PAGES = {59-68},
URL = {http://dx.doi.org/10.1145/299432.299457},
NOTE = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.95.9151},
KEYWORDS = {abstract network, from quartets, phylogenetic network, phylogeny, polynomial, Program SplitsTree, reconstruction, split network, weakly compatible}
}

1998

1

Daniel H. Huson. SplitsTree: analyzing and visualizing evolutionary data. In BIO, Vol. 14(1):68-73, 1998.
Keywords: abstract network, phylogenetic network, phylogeny, Program SplitsTree, software, split network.
Note: http://bioweb.pasteur.fr/docs/doc-gensoft/splitstree/splitstree.ps.

@Article{Huson1998,
AUTHOR = {Huson, Daniel H.},
TITLE = {SplitsTree: analyzing and visualizing evolutionary data},
YEAR = {1998},
JOURNAL = {BIO},
VOLUME = {14},
NUMBER = {1},
PAGES = {68-73},
URL = {http://dx.doi.org/10.1093/bioinformatics/14.1.68},
NOTE = {http://bioweb.pasteur.fr/docs/doc-gensoft/splitstree/splitstree.ps},
ANNOTE = {CITE : },
KEYWORDS = {abstract network, phylogenetic network, phylogeny, Program SplitsTree, software, split network}
}

2

John Kececioglu and Dan Gusfield. Reconstructing a history of recombinations from a set of sequences. In DAM, Pages 239-260, 1998.
Keywords: from sequences, NP complete, polynomial, recombination, reconstruction.
Note: http://citeseer.ist.psu.edu/76600.html.

@Article{KececiogluGusfield1998,
AUTHOR = {Kececioglu, John and Gusfield, Dan},
TITLE = {Reconstructing a history of recombinations from a set of sequences},
YEAR = {1998},
JOURNAL = {DAM},
PAGES = {239-260},
URL = {http://dx.doi.org/10.1016/S0166-218X(98)00074-2},
NOTE = {http://citeseer.ist.psu.edu/76600.html},
ANNOTE = {BIBUPDATE : 20070917},
KEYWORDS = {from sequences, NP complete, polynomial, recombination, reconstruction}
}

3

Roderic D.M. Page and Michael A. Charleston. Trees within trees: phylogeny and historical associations. In TEE, Vol. 13(9):356-359, 1998.
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, reconstruction, survey.
Note: http://taxonomy.zoology.gla.ac.uk/rod/papers/tree.pdf.

@Article{PageCharleston1998,
AUTHOR = {Page, Roderic D.M. and Charleston, Michael A.},
TITLE = {Trees within trees: phylogeny and historical associations},
YEAR = {1998},
JOURNAL = {TEE},
VOLUME = {13},
NUMBER = {9},
PAGES = {356-359},
URL = {http://dx.doi.org/10.1016/s0169-5347(98)01438-4},
NOTE = {http://taxonomy.zoology.gla.ac.uk/rod/papers/tree.pdf},
ANNOTE = {BIBUPDATE : 20081127},
KEYWORDS = {duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, reconstruction, survey}
}

4

Bin Ma, Lusheng Wang and Ming Li. Fixed topology alignment with recombination. In CPM98, Vol. 1448:174-188 of LNCS, springer, 1998.
Keywords: approximation, explicit network, from network, from sequences, galled tree, inapproximability, phylogenetic network, phylogeny, recombination.
Note: http://dx.doi.org/10.1007/BFb0030789.

@InProceedings{MWL1998,
AUTHOR = {Ma, Bin and Wang, Lusheng and Li, Ming},
TITLE = {Fixed topology alignment with recombination},
YEAR = {1998},
BOOKTITLE = {CPM98},
VOLUME = {1448},
PAGES = {174-188},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/BFb0030789},
NOTE = {http://dx.doi.org/10.1007/BFb0030789},
ANNOTE = {BIBUPDATE : 20081225},
KEYWORDS = {approximation, explicit network, from network, from sequences, galled tree, inapproximability, phylogenetic network, phylogeny, recombination}
}

1997

1

David Bryant. Building Trees, Hunting for Trees, and Comparing Trees: theory and method in phylogenetic analysis. PhD thesis, Dept. Mathematics, University of Canterbury, New Zealand, 1997.
Note: http://citeseer.ist.psu.edu/685475.html.

@PhdThesis{Bryant1997,
AUTHOR = {Bryant, David},
TITLE = {Building Trees, Hunting for Trees, and Comparing Trees: theory and method in phylogenetic analysis},
YEAR = {1997},
SCHOOL = {Dept. Mathematics, University of Canterbury, New Zealand},
NOTE = {http://citeseer.ist.psu.edu/685475.html},
ANNOTE = {CITE : }
}

2

Andreas W. M. Dress, Katharina Huber and Vincent Moulton. Some Variations on a Theme by Buneman. In ACOM, Vol. 1:339-352, 1997.
Note: http://dx.doi.org/10.1007/BF02558485.

@Article{DHM1997,
AUTHOR = {Dress, Andreas W. M. and Huber, Katharina and Moulton, Vincent},
TITLE = {Some Variations on a Theme by Buneman},
YEAR = {1997},
JOURNAL = {ACOM},
VOLUME = {1},
PAGES = {339-352},
URL = {http://dx.doi.org/10.1007/BF02558485},
NOTE = {http://dx.doi.org/10.1007/BF02558485},
ANNOTE = {BIBUPDATE : 20070919}
}

3

Walter M. Fitch. Networks and viral evolution. In JME, Vol. 44(Suppl. 1):S65-S75, 1997.
Keywords: netting, parsimony, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1007/PL00000059.

@Article{Fitch1997,
AUTHOR = {Fitch, Walter M.},
TITLE = {Networks and viral evolution},
YEAR = {1997},
JOURNAL = {JME},
VOLUME = {44},
NUMBER = {Suppl. 1},
PAGES = {S65-S75},
URL = {http://dx.doi.org/10.1007/PL00000059},
NOTE = {http://dx.doi.org/10.1007/PL00000059},
ANNOTE = {BIBUPDATE : 20070918},
KEYWORDS = {netting, parsimony, phylogenetic network, phylogeny, reconstruction}
}

4

Andreas W. M. Dress, Mike Hendy, Katharina Huber and Vincent Moulton. On the number of vertices and edges in the Buneman graph. In ACOM, Vol. 1:329-337, 1997.
Keywords: abstract network, median network, phylogenetic network, phylogeny, split.
Note: http://dx.doi.org/10.1007/BF02558484.

@Article{DHHM1997,
AUTHOR = {Dress, Andreas W. M. and Hendy, Mike and Huber, Katharina and Moulton, Vincent},
TITLE = {On the number of vertices and edges in the Buneman graph},
YEAR = {1997},
JOURNAL = {ACOM},
VOLUME = {1},
PAGES = {329-337},
URL = {http://dx.doi.org/10.1007/BF02558484},
NOTE = {http://dx.doi.org/10.1007/BF02558484},
ANNOTE = {BIBUPDATE : 20071122},
KEYWORDS = {abstract network, median network, phylogenetic network, phylogeny, split}
}

5

Wayne P. Maddison. Gene Trees in Species Trees. In Systematic Biology, Vol. 46(3):523-536, 1997.
Keywords: from rooted trees, from species tree, lateral gene transfer, phylogeny, reconstruction, time consistent network.
Note: http://dx.doi.org/10.2307/2413694.

@Article{Maddison1997,
AUTHOR = {Maddison, Wayne P.},
TITLE = {Gene Trees in Species Trees},
YEAR = {1997},
JOURNAL = {Systematic Biology},
VOLUME = {46},
NUMBER = {3},
PAGES = {523-536},
URL = {http://dx.doi.org/10.2307/2413694},
NOTE = {http://dx.doi.org/10.2307/2413694},
ANNOTE = {CITE : },
KEYWORDS = {from rooted trees, from species tree, lateral gene transfer, phylogeny, reconstruction, time consistent network}
}

1996

1

Andreas W. M. Dress, Daniel H. Huson and Vincent Moulton. Analyzing and visualizing distance data using SplitsTree. In DAM, Vol. 71(1):95-109, 1996.
Keywords: abstract network, from distances, phylogenetic network, phylogeny, Program SplitsTree, software, split network, visualization.
Note: http://bibiserv.techfak.uni-bielefeld.de/splits/splits.pdf.

@Article{DHM1996,
AUTHOR = {Dress, Andreas W. M. and Huson, Daniel H. and Moulton, Vincent},
TITLE = {Analyzing and visualizing distance data using SplitsTree},
YEAR = {1996},
JOURNAL = {DAM},
VOLUME = {71},
NUMBER = {1},
PAGES = {95-109},
URL = {http://dx.doi.org/10.1016/S0166-218X(96)00059-5},
NOTE = {http://bibiserv.techfak.uni-bielefeld.de/splits/splits.pdf},
ANNOTE = {BIBUPDATE : 20070927},
KEYWORDS = {abstract network, from distances, phylogenetic network, phylogeny, Program SplitsTree, software, split network, visualization}
}

2

Paul Marjoram and Robert C. Griffiths. Ancestral inference from samples of DNA sequences with recombination. In JCB, Vol. 3(4):479-502, 1996.
Keywords: ARG, phylogenetic network, phylogeny, statistical model.
Note: http://www.math.canterbury.ac.nz/~r.sainudiin/recomb/JCB_paper.pdf.

@Article{GriffithsMarjoram1996,
AUTHOR = {Marjoram, Paul and Griffiths, Robert C.},
TITLE = {Ancestral inference from samples of DNA sequences with recombination},
YEAR = {1996},
JOURNAL = {JCB},
VOLUME = {3},
NUMBER = {4},
PAGES = {479-502},
URL = {http://dx.doi.org/10.1089/cmb.1996.3.479},
NOTE = {http://www.math.canterbury.ac.nz/~r.sainudiin/recomb/JCB_paper.pdf},
ANNOTE = {CITE : },
KEYWORDS = {ARG, phylogenetic network, phylogeny, statistical model}
}

1995

1

Hans-Jürgen Bandelt. Combination of data in phylogenetic analysis. In PSE, Vol. Supp. 9:336-361, 1995.
Keywords: from trees, phylogenetic network, phylogeny, reconstruction.

@Article{Bandelt1995,
AUTHOR = {Bandelt, Hans-J{\~A}�rgen},
TITLE = {Combination of data in phylogenetic analysis},
YEAR = {1995},
JOURNAL = {PSE},
VOLUME = {Supp. 9},
PAGES = {336-361},
URL = {http://dx.doi.org/10.1007/978-3-7091-6612-3_38},
ANNOTE = {CITE : },
KEYWORDS = {from trees, phylogenetic network, phylogeny, reconstruction}
}

2

Hans-Jürgen Bandelt, Peter Forster, Bryan C. Sykes and Martin Richards. Mitochondrial portraits of human population using median networks. In GEN, Vol. 141:743-753, 1995.
Keywords: from splits, median network, population genetics, Program Spectronet, reconstruction, visualization.
Note: http://www.genetics.org/cgi/content/abstract/141/2/743.

@Article{BFSR1995,
AUTHOR = {Bandelt, Hans-J{\~A}�rgen and Forster, Peter and Sykes, Bryan C. and Richards, Martin},
TITLE = {Mitochondrial portraits of human population using median networks},
YEAR = {1995},
JOURNAL = {GEN},
VOLUME = {141},
PAGES = {743-753},
URL = {http://www.ncbi.nlm.nih.gov/pubmed/8647407},
NOTE = {http://www.genetics.org/cgi/content/abstract/141/2/743},
ANNOTE = {CITE : },
KEYWORDS = {from splits, median network, population genetics, Program Spectronet, reconstruction, visualization}
}

3

Rainer Wetzel. Zur Visualisierung abstrakter Ahnlichkeitsbeziehungen. PhD thesis, Universität Bielefeld, Germany, 1995.
Keywords: abstract network, circular split system, visualization.

@PhdThesis{Wetzel1995,
AUTHOR = {Wetzel, Rainer},
TITLE = {Zur Visualisierung abstrakter Ahnlichkeitsbeziehungen},
YEAR = {1995},
SCHOOL = {Universit{\~A}�t Bielefeld, Germany},
ANNOTE = {CITE : },
KEYWORDS = {abstract network, circular split system, visualization}
}

4

Daniel H. Huson and Rainer Wetzel. Analyzing and visualizing sequence and distance data with SplitsTree V1.0.2. 1995.
Keywords: abstract network, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, software, split network, visualization.
Note: Technical report, http://citeseer.ist.psu.edu/173442.html.

@Misc{HusonWetzel1995,
AUTHOR = {Huson, Daniel H. and Wetzel, Rainer},
TITLE = {Analyzing and visualizing sequence and distance data with SplitsTree V1.0.2},
YEAR = {1995},
NOTE = {Technical report, http://citeseer.ist.psu.edu/173442.html},
ANNOTE = {CITE : },
KEYWORDS = {abstract network, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, software, split network, visualization}
}

5

Loren H. Rieseberg and James D. Morefield. Character expression, phylogenetic reconstruction, and the detection of reticulate evolution. In P. C. Hoch and A. G. Stephenson editors, Experimental and molecular approaches to plant biosystematics, Pages 333–353, 1995.
Keywords: hybridization, phylogeny, Program Reticlad.
Note: http://www3.botany.ubc.ca/rieseberglab/loren pubs/1995 Chapter in Experimental and Molecular approaches to Plant Biosystematics.pdf.

@InBook{RiesebergMorefield1995,
AUTHOR = {Rieseberg, Loren H. and Morefield, James D.},
TITLE = {Character expression, phylogenetic reconstruction, and the detection of reticulate evolution},
YEAR = {1995},
BOOKTITLE = {Experimental and molecular approaches to plant biosystematics},
PAGES = {333{\^a}��353},
EDITOR = {Hoch, P. C. and Stephenson, A. G.},
SERIES = {Monographs in Systematic Botany at the Missouri Botanical Garden},
NOTE = {http://www3.botany.ubc.ca/rieseberglab/loren pubs/1995 Chapter in Experimental and Molecular approaches to Plant Biosystematics.pdf},
ANNOTE = {BIBUPDATE : 20080404},
KEYWORDS = {hybridization, phylogeny, Program Reticlad}
}

1994

1

Hans-Jürgen Bandelt. Phylogenetic Networks. In Verhandlungen des Naturwissenschaftlichen Vereins Hamburg, Vol. 34:51-71, 1994.

@InProceedings{Bandelt1994,
AUTHOR = {Bandelt, Hans-J{\~A}�rgen},
TITLE = {Phylogenetic Networks},
YEAR = {1994},
BOOKTITLE = {Verhandlungen des Naturwissenschaftlichen Vereins Hamburg},
VOLUME = {34},
PAGES = {51-71},
ANNOTE = {CITE : }
}

2

Hans-Jürgen Bandelt and Andreas W. M. Dress. An order theoretic framework for overlapping clustering. In DM, Vol. 136(1-3):21-37, 1994.

Toggle abstract

@Article{BandeltDress1994,
AUTHOR = {Bandelt, Hans-J{\~A}�rgen and Dress, Andreas W. M.},
TITLE = {An order theoretic framework for overlapping clustering},
YEAR = {1994},
JOURNAL = {DM},
VOLUME = {136},
NUMBER = {1-3},
PAGES = {21-37},
URL = {http://dx.doi.org/10.1016/0012-365X(94)00105-R},
ANNOTE = {CITE : }
}

3

John Kececioglu and Dan Gusfield. Reconstructing a history of recombinations from a set of sequences. In SODA94, Pages 471-480, 1994.
Keywords: from sequences, NP complete, polynomial, recombination, reconstruction.
Note: http://portal.acm.org/citation.cfm?id=314626#.

@InProceedings{KececiogluGusfield1994,
AUTHOR = {Kececioglu, John and Gusfield, Dan},
TITLE = {Reconstructing a history of recombinations from a set of sequences},
YEAR = {1994},
BOOKTITLE = {SODA94},
PAGES = {471-480},
NOTE = {http://portal.acm.org/citation.cfm?id=314626#},
ANNOTE = {CITE : },
KEYWORDS = {from sequences, NP complete, polynomial, recombination, reconstruction}
}

4

Laurent Excoffier and Peter E. Smouse. Using Allele Frequencies and Geographic Subdivision to Reconstruct Gene Trees Within a Species: Molecular Variance Parsimony. In GEN, Vol. 136:343-359, 1994.
Keywords: from distances, minimum spanning network, phylogenetic network, phylogeny, Program Arlequin, reconstruction, software.
Note: http://www.genetics.org/cgi/content/abstract/136/1/343.

@Article{ExcoffierSmouse1994,
AUTHOR = {Excoffier, Laurent and Smouse, Peter E.},
TITLE = {Using Allele Frequencies and Geographic Subdivision to Reconstruct Gene Trees Within a Species: Molecular Variance Parsimony},
YEAR = {1994},
JOURNAL = {GEN},
VOLUME = {136},
PAGES = {343-359},
NOTE = {http://www.genetics.org/cgi/content/abstract/136/1/343},
ANNOTE = {CITE : },
KEYWORDS = {from distances, minimum spanning network, phylogenetic network, phylogeny, Program Arlequin, reconstruction, software}
}

5

Zdenek Skála and Jan Zrzavý. Phylogenetic reticulations and cladistics: discussion of methodological concepts. In Cladistics, Vol. 10(3):305-313, 1994.
Keywords: explicit network, from rooted trees, from species tree, parsimony, phylogeny.
Note: http://dx.doi.org/10.1111/j.1096-0031.1994.tb00180.x.

@Article{SkalaZrzavy1994,
AUTHOR = {Sk{\~A}�la, Zdenek and Zrzav{\~A}�, Jan},
TITLE = {Phylogenetic reticulations and cladistics: discussion of methodological concepts},
YEAR = {1994},
JOURNAL = {Cladistics},
VOLUME = {10},
NUMBER = {3},
PAGES = {305-313},
URL = {http://dx.doi.org/10.1111/j.1096-0031.1994.tb00180.x},
NOTE = {http://dx.doi.org/10.1111/j.1096-0031.1994.tb00180.x},
KEYWORDS = {explicit network, from rooted trees, from species tree, parsimony, phylogeny}
}

6

Hans-Jürgen Bandelt and Andreas W. M. Dress. A relational approach to split decomposition. In H.-H. Bock, W. Lenski and M. M. Richter editors, Information Systems and Data Analysis, Proceedings of the 17th Annual Conference of the Gesellschaft Für Klassifikation (GFKL93), Vol. 42:123-131 of Studies in Classification, Data Analysis, and Knowledge Organization, springer, 1994.
Keywords: characterization, from quartets, phylogenetic network, weakly compatible.

@InProceedings{BandeltDress1994b,
AUTHOR = {Bandelt, Hans-J{\~A}�rgen and Dress, Andreas W. M.},
TITLE = {A relational approach to split decomposition},
YEAR = {1994},
BOOKTITLE = {Information Systems and Data Analysis, Proceedings of the 17th Annual Conference of the Gesellschaft F{\~A}�r Klassifikation (GFKL93)},
VOLUME = {42},
PAGES = {123-131},
EDITOR = {Bock, H.-H. and Lenski, W. and Richter, M. M.},
SERIES = {Studies in Classification, Data Analysis, and Knowledge Organization},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-642-50974-2_13},
KEYWORDS = {characterization, from quartets, phylogenetic network, weakly compatible}
}

1993

1

Joaquin Dopazo, Andreas W. M. Dress and Arndt von Haeseler. Split decomposition: a new technique to analyse viral evolution. In PNAS, Vol. 90:10320-10324, 1993.
Keywords: abstract network, phylogenetic network, phylogeny, split, split decomposition, split network, visualization.
Note: http://dx.doi.org/10.1073/pnas.90.21.10320.

@Article{DDH1993,
AUTHOR = {Dopazo, Joaquin and Dress, Andreas W. M. and von Haeseler, Arndt},
TITLE = {Split decomposition: a new technique to analyse viral evolution},
YEAR = {1993},
JOURNAL = {PNAS},
VOLUME = {90},
PAGES = {10320-10324},
URL = {http://dx.doi.org/10.1073/pnas.90.21.10320},
NOTE = {http://dx.doi.org/10.1073/pnas.90.21.10320},
ANNOTE = {BIBUPDATE : 20070927},
KEYWORDS = {abstract network, phylogenetic network, phylogeny, split, split decomposition, split network, visualization}
}

2

Arndt von Haeseler and Gary A. Churchill. Network models for sequence evolution. In JME, Vol. 37(1):77-85, 1993.
Keywords: explicit network, likelihood, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: http://dx.doi.org/10.1007/BF00170465.

@Article{HaeselerChurchill1993,
AUTHOR = {von Haeseler, Arndt and Churchill, Gary A.},
TITLE = {Network models for sequence evolution},
YEAR = {1993},
JOURNAL = {JME},
VOLUME = {37},
NUMBER = {1},
PAGES = {77-85},
URL = {http://dx.doi.org/10.1007/BF00170465},
NOTE = {http://dx.doi.org/10.1007/BF00170465},
ANNOTE = {BIBUPDATE : 20070918},
KEYWORDS = {explicit network, likelihood, phylogenetic network, phylogeny, reconstruction, statistical model}
}

3

Jotun Hein. A heuristic method to reconstruct the history of sequences subject to recombination. In JME, Vol. 36(4):396-405, 1993.
Keywords: explicit network, from sequences, heuristic, parsimony, phylogenetic network, phylogeny, Program RecPars, recombination, recombination detection, software.
Note: http://dx.doi.org/10.1007/BF00182187.

@Article{Hein1993,
AUTHOR = {Hein, Jotun},
TITLE = {A heuristic method to reconstruct the history of sequences subject to recombination},
YEAR = {1993},
JOURNAL = {JME},
VOLUME = {36},
NUMBER = {4},
PAGES = {396-405},
URL = {http://dx.doi.org/10.1007/BF00182187},
NOTE = {http://dx.doi.org/10.1007/BF00182187},
ANNOTE = {CITE : },
KEYWORDS = {explicit network, from sequences, heuristic, parsimony, phylogenetic network, phylogeny, Program RecPars, recombination, recombination detection, software}
}

1992

1

Hans-Jürgen Bandelt and Andreas W. M. Dress. A canonical decomposition theory for metrics on a finite set. In Advances in Mathematics, Vol. 92(1):47-105, 1992.
Keywords: abstract network, circular split system, from distances, split, split decomposition, split network, weak hierarchy, weakly compatible.

Toggle abstract

@Article{BandeltDress1992,
AUTHOR = {Bandelt, Hans-J{\~A}�rgen and Dress, Andreas W. M.},
TITLE = {A canonical decomposition theory for metrics on a finite set},
YEAR = {1992},
JOURNAL = {Advances in Mathematics},
VOLUME = {92},
NUMBER = {1},
PAGES = {47-105},
URL = {http://dx.doi.org/10.1016/0001-8708(92)90061-O},
ANNOTE = {CITE : },
KEYWORDS = {abstract network, circular split system, from distances, split, split decomposition, split network, weak hierarchy, weakly compatible}
}

2

Hans-Jürgen Bandelt and Andreas W. M. Dress. Split Decomposition: A new and useful approach to phylogenetic analysis of distance data. In MPE, Vol. 1(3):242-252, 1992.
Keywords: abstract network, from distances, phylogenetic network, phylogeny, reconstruction, split, split decomposition, split network.
Note: http://dx.doi.org/10.1016/1055-7903(92)90021-8.

Toggle abstract

@Article{BandeltDress1992b,
AUTHOR = {Bandelt, Hans-J{\~A}�rgen and Dress, Andreas W. M.},
TITLE = {Split Decomposition: A new and useful approach to phylogenetic analysis of distance data},
YEAR = {1992},
JOURNAL = {MPE},
VOLUME = {1},
NUMBER = {3},
PAGES = {242-252},
URL = {http://dx.doi.org/10.1016/1055-7903(92)90021-8},
NOTE = {http://dx.doi.org/10.1016/1055-7903(92)90021-8},
ANNOTE = {CITE : },
KEYWORDS = {abstract network, from distances, phylogenetic network, phylogeny, reconstruction, split, split decomposition, split network}
}

3

Lucinda A. McDade. Hybrids and phylogenetic systematics II. The impact of hybrids on cladistic analysis. In Evolution, Vol. 46(5):1329-1346, 1992.
Keywords: explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny.
Note: http://www.jstor.org/stable/2409940.

@Article{McDade1992,
AUTHOR = {McDade, Lucinda A.},
TITLE = {Hybrids and phylogenetic systematics II. The impact of hybrids on cladistic analysis},
YEAR = {1992},
JOURNAL = {Evolution},
VOLUME = {46},
NUMBER = {5},
PAGES = {1329-1346},
URL = {http://dx.doi.org/10.2307/2409940},
NOTE = {http://www.jstor.org/stable/2409940},
KEYWORDS = {explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny}
}

4

Hans-Jürgen Bandelt. Four-point characterization of the dissimilarity functions obtained from indexed closed weak hierarchies. 1992.
Keywords: characterization, clustering, from distances, pyramid, weak hierarchy.
Note: Mathematisches Seminar, Universität Hamburg.

@Misc{Bandelt1992,
AUTHOR = {Bandelt, Hans-J{\~A}�rgen},
TITLE = {Four-point characterization of the dissimilarity functions obtained from indexed closed weak hierarchies},
YEAR = {1992},
NOTE = {Mathematisches Seminar, Universit{\~A}�t Hamburg},
KEYWORDS = {characterization, clustering, from distances, pyramid, weak hierarchy}
}

1990

1

Patrice Bertrand and Edwin Diday. Une généralisation des arbres hiérarchiques~: les représentations pyramidales. In Revue de Statistique Appliquée, Vol. 38(3):53-78, 1990.
Note: http://www.numdam.org/item?id=RSA_1990__38_3_53_0.

@Article{BertrandDiday1990,
AUTHOR = {Bertrand, Patrice and Diday, Edwin},
TITLE = {Une g{\~A}�n{\~A}�ralisation des arbres hi{\~A}�rarchiques~: les repr{\~A}�sentations pyramidales},
YEAR = {1990},
JOURNAL = {Revue de Statistique Appliqu{\~A}�e},
VOLUME = {38},
NUMBER = {3},
PAGES = {53-78},
NOTE = {http://www.numdam.org/item?id=RSA_1990__38_3_53_0},
ANNOTE = {CITE : }
}

2

Jotun Hein. Reconstructing evolution of sequences subject to recombination using parsimony. In MBIO, Vol. 98(2):185-200, 1990.
Note: http://dx.doi.org/10.1016/0025-5564(90)90123-G.

Toggle abstract

@Article{Hein1990,
AUTHOR = {Hein, Jotun},
TITLE = {Reconstructing evolution of sequences subject to recombination using parsimony},
YEAR = {1990},
JOURNAL = {MBIO},
VOLUME = {98},
NUMBER = {2},
PAGES = {185-200},
URL = {http://dx.doi.org/10.1016/0025-5564(90)90123-G},
NOTE = {http://dx.doi.org/10.1016/0025-5564(90)90123-G},
ANNOTE = {CITE : }
}

1989

1

Hans-Jürgen Bandelt and Andreas W. M. Dress. Weak hierarchies associated with similarity measures: an additive clustering technique. In BMB, Vol. 51:113-166, 1989.
Keywords: abstract network, clustering, from distances, from trees, phylogenetic network, phylogeny, Program WeakHierarchies, reconstruction, weak hierarchy.
Note: http://dx.doi.org/10.1007/BF02458841.

Toggle abstract

@Article{BandeltDress1989,
AUTHOR = {Bandelt, Hans-J{\~A}�rgen and Dress, Andreas W. M.},
TITLE = {Weak hierarchies associated with similarity measures: an additive clustering technique},
YEAR = {1989},
JOURNAL = {BMB},
VOLUME = {51},
PAGES = {113-166},
URL = {http://dx.doi.org/10.1007/BF02458841},
NOTE = {http://dx.doi.org/10.1007/BF02458841},
ANNOTE = {BIBUPDATE : 20070920},
KEYWORDS = {abstract network, clustering, from distances, from trees, phylogenetic network, phylogeny, Program WeakHierarchies, reconstruction, weak hierarchy}
}

1986

1

Patrice Bertrand. Étude de la représentation pyramidale. PhD thesis, Université de Paris-Dauphine, France, 1986.
Keywords: abstract network, pyramid.

@PhdThesis{Bertrand1986,
AUTHOR = {Bertrand, Patrice},
TITLE = {{\~A}�tude de la repr{\~A}�sentation pyramidale},
YEAR = {1986},
SCHOOL = {Universit{\~A}� de Paris-Dauphine, France},
ANNOTE = {CITE : },
KEYWORDS = {abstract network, pyramid}
}

2

Ingo Althöfer. On optimal realizations of finite metric spaces by graphs. In Discrete and Computational Geometry, Vol. 3(1):103-122, 1986.
Keywords: NP complete, optimal realization, realization.
Note: http://dx.doi.org/10.1007/BF02187901.

Toggle abstract

@Article{Althoefer1986,
AUTHOR = {Alth{\~A}�fer, Ingo},
TITLE = {On optimal realizations of finite metric spaces by graphs},
YEAR = {1986},
JOURNAL = {Discrete and Computational Geometry},
VOLUME = {3},
NUMBER = {1},
PAGES = {103-122},
URL = {http://dx.doi.org/10.1007/BF02187901},
NOTE = {http://dx.doi.org/10.1007/BF02187901},
ANNOTE = {BIBUPDATE : 20080513},
KEYWORDS = {NP complete, optimal realization, realization}
}

3

Alain Guénoche. Graphical Representation of a Boolean Array. In Computers and the Humanities, Vol. 20(4):277-281, 1986.
Keywords: from splits, median network, reconstruction.
Note: http://dx.doi.org/10.1007/BF02400118.

Toggle abstract

@Article{Guenoche1986,
AUTHOR = {Gu{\~A}�noche, Alain},
TITLE = {Graphical Representation of a Boolean Array},
YEAR = {1986},
JOURNAL = {Computers and the Humanities},
VOLUME = {20},
NUMBER = {4},
PAGES = {277-281},
URL = {http://dx.doi.org/10.1007/BF02400118},
NOTE = {http://dx.doi.org/10.1007/BF02400118},
KEYWORDS = {from splits, median network, reconstruction}
}

1985

1

Patrice Bertrand and Edwin Diday. A visual representation of the compatibility between an order and a dissimilarity index: the pyramids. In CSQ, Vol. 2:31-42, 1985.
Keywords: pyramid.

@Article{BertrandDiday1985,
AUTHOR = {Bertrand, Patrice and Diday, Edwin},
TITLE = {A visual representation of the compatibility between an order and a dissimilarity index: the pyramids},
YEAR = {1985},
JOURNAL = {CSQ},
VOLUME = {2},
PAGES = {31-42},
ANNOTE = {CITE : },
KEYWORDS = {pyramid}
}

2

Richard R. Hudson and Norman L. Kaplan. Statistical Properties of the Number of Recombination Events in the History of a Sample of DNA Sequences. In GEN, Vol. 111:147-164, 1985.
Note: http://www.genetics.org/cgi/content/abstract/111/1/147.

@Article{HudsonKaplan1985,
AUTHOR = {Hudson, Richard R. and Kaplan, Norman L.},
TITLE = {Statistical Properties of the Number of Recombination Events in the History of a Sample of DNA Sequences},
YEAR = {1985},
JOURNAL = {GEN},
VOLUME = {111},
PAGES = {147-164},
URL = {http://www.ncbi.nlm.nih.gov/pubmed/4029609},
NOTE = {http://www.genetics.org/cgi/content/abstract/111/1/147},
ANNOTE = {CITE : }
}

3

Victoria A. Funk. Phylogenetic patterns and hybridization. In Annals of the Missouri Botanical Garden, Vol. 72(4):681-715, 1985.
Keywords: explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny.
Note: http://www.jstor.org/stable/2399220.

@Article{Funk1985,
AUTHOR = {Funk, Victoria A.},
TITLE = {Phylogenetic patterns and hybridization},
YEAR = {1985},
JOURNAL = {Annals of the Missouri Botanical Garden},
VOLUME = {72},
NUMBER = {4},
PAGES = {681-715},
URL = {http://dx.doi.org/10.2307/2399220},
NOTE = {http://www.jstor.org/stable/2399220},
KEYWORDS = {explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny}
}

1983

1

Richard R. Hudson. Properties of the neutral allele model with intragenic recombination. In TPP, Vol. 23:183-201, 1983.
Keywords: coalescent.
Note: http://dx.doi.org/10.1016/0040-5809(83)90013-8, see also http://www.brics.dk/~compbio/coalescent/hudson_animator.html.

Toggle abstract

@Article{Hudson1983,
AUTHOR = {Hudson, Richard R.},
TITLE = {Properties of the neutral allele model with intragenic recombination},
YEAR = {1983},
JOURNAL = {TPP},
VOLUME = {23},
PAGES = {183-201},
URL = {http://dx.doi.org/10.1016/0040-5809(83)90013-8},
NOTE = {http://dx.doi.org/10.1016/0040-5809(83)90013-8, see also http://www.brics.dk/~compbio/coalescent/hudson_animator.html},
ANNOTE = {CITE : },
KEYWORDS = {coalescent}
}

2

Gareth J. Nelson. Reticulation in Cladograms. In Advances in Cladistics: Proceedings of the Second meeting of the Willi Hennig Society (HENNIG II), Pages 105-111, Columbia University Press, 1983.
Keywords: explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny.

@InProceedings{Nelson1983,
AUTHOR = {Nelson, Gareth J.},
TITLE = {Reticulation in Cladograms},
YEAR = {1983},
BOOKTITLE = {Advances in Cladistics: Proceedings of the Second meeting of the Willi Hennig Society (HENNIG II)},
PAGES = {105-111},
PUBLISHER = {Columbia University Press},
ANNOTE = {CITE : },
KEYWORDS = {explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny}
}

3

Hans-Erik Wanntorp. Reticulated cladograms and the identification of hybrid taxa. In Advances in Cladistics: Proceedings of the Second meeting of the Willi Hennig Society (HENNIG II), Pages 81-88, Columbia University Press, 1983.
Keywords: explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny.

@InProceedings{Wanntorp1983,
AUTHOR = {Wanntorp, Hans-Erik},
TITLE = {Reticulated cladograms and the identification of hybrid taxa},
YEAR = {1983},
BOOKTITLE = {Advances in Cladistics: Proceedings of the Second meeting of the Willi Hennig Society (HENNIG II)},
PAGES = {81-88},
PUBLISHER = {Columbia University Press},
ANNOTE = {CITE : },
KEYWORDS = {explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny}
}

4

Christopher J. Humphries. Primary data in hybrid analysis. In Advances in Cladistics: Proceedings of the Second meeting of the Willi Hennig Society (HENNIG II), Pages 89-103, Columbia University Press, 1983.
Keywords: explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny.

@InProceedings{Humphries1983,
AUTHOR = {Humphries, Christopher J.},
TITLE = {Primary data in hybrid analysis},
YEAR = {1983},
BOOKTITLE = {Advances in Cladistics: Proceedings of the Second meeting of the Willi Hennig Society (HENNIG II)},
PAGES = {89-103},
PUBLISHER = {Columbia University Press},
KEYWORDS = {explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny}
}

5

Warren H. Wagner. Reticulistics: the recognition of hybrids and their role in cladistics and classification. In Advances in Cladistics: Proceedings of the Second meeting of the Willi Hennig Society (HENNIG II), Pages 63-79, 1983.
Keywords: explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny.

@InProceedings{Wagner1983,
AUTHOR = {Wagner, Warren H.},
TITLE = {Reticulistics: the recognition of hybrids and their role in cladistics and classification},
YEAR = {1983},
BOOKTITLE = {Advances in Cladistics: Proceedings of the Second meeting of the Willi Hennig Society (HENNIG II)},
PAGES = {63-79},
KEYWORDS = {explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny}
}

1979

1

Kare Bremer and Hans-Erik Wanntorp. Hierarchy and reticulation in systematics. In Systematic Zoology, Vol. 28(4):624-627, 1979.
Keywords: explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny.
Note: http://dx.doi.org/10.2307/2412572.

@Article{BremerWanntorp1979,
AUTHOR = {Bremer, Kare and Wanntorp, Hans-Erik},
TITLE = {Hierarchy and reticulation in systematics},
YEAR = {1979},
JOURNAL = {Systematic Zoology},
VOLUME = {28},
NUMBER = {4},
PAGES = {624-627},
URL = {http://dx.doi.org/10.2307/2412572},
NOTE = {http://dx.doi.org/10.2307/2412572},
KEYWORDS = {explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny}
}

1975

1

Peter H. A. Sneath. Cladistic Representation of Reticulate Evolution. In Systematic Zoology, Vol. 24(3):165-173, 1975.
Keywords: explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny.
Note: http://dx.doi.org/10.2307/2412721.

@Article{Sneath1975,
AUTHOR = {Sneath, Peter H. A.},
TITLE = {Cladistic Representation of Reticulate Evolution},
YEAR = {1975},
JOURNAL = {Systematic Zoology},
VOLUME = {24},
NUMBER = {3},
PAGES = {165-173},
URL = {http://dx.doi.org/10.2307/2412721},
NOTE = {http://dx.doi.org/10.2307/2412721},
ANNOTE = {CITE : },
KEYWORDS = {explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny}
}

1971

1

Verne Grant. Plant Speciation. Pages 300-320,383-386, Columbia University Press, 1971.
Keywords: hybridization, phylogenetic network, phylogeny.

@InBook{Grant1971,
AUTHOR = {Grant, Verne},
TITLE = {Plant Speciation},
YEAR = {1971},
PAGES = {300-320,383-386},
PUBLISHER = {Columbia University Press},
ANNOTE = {BIBUPDATE : 20070922},
KEYWORDS = {hybridization, phylogenetic network, phylogeny}
}

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