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

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Article (Journal)

1

@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

@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}
}

3

@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}
}

4

@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}
}

5

@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}
}

6

@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}
}

7

@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 : }
}

8

@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 : }
}

9

@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}
}

10

@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 : }
}

11

@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}
}

12

@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}
}

13

@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}
}

14

@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}
}

15

@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}
}

16

@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}
}

17

@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}
}

18

@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}
}

19

@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}
}

20

@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}
}

21

@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}
}

22

@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}
}

23

@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}
}

24

@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}
}

25

@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}
}

26

@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}
}

27

@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}
}

28

@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}
}

29

@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}
}

30

@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}
}

31

@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}
}

32

@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 : }
}

33

@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}
}

34

@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}
}

35

@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}
}

36

@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}
}

37

@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}
}

38

@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}
}

39

@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}
}

40

@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}
}

41

@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}
}

42

@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},
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KEYWORDS = {abstract network, from distances, phylogenetic network, phylogeny, Program T REX, reticulogram}
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TITLE = {Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy},
YEAR = {2004},
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TITLE = {Networks in phylogenetic analysis: new tools for population biology},
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TITLE = {Fast Algorithms for computing the Tripartition-based Distance between Phylogenetic Networks},
YEAR = {2007},
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KEYWORDS = {explicit network, from sequences, labeling, NP complete, parsimony, phylogenetic network, phylogeny}
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AUTHOR = {Nakhleh, Luay and Ringe, Don and Warnow, Tandy},
TITLE = {Perfect Phylogenetic Networks: A New Methodology for Reconstructing the Evolutionary History of Natural Languages},
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103

@Article{WBLHM2005,
AUTHOR = {Winkworth, Richard C. and Bryant, David and Lockhart, Peter J. and Havell, David and Moulton, Vincent},
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KEYWORDS = {abstract network, from distances, from network, phylogenetic network, phylogeny, reconstruction, split, split network}
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104

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KEYWORDS = {from distances, from network, labeling, phylogenetic network, phylogeny}
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105

@Article{Willson2006b,
AUTHOR = {Willson, Stephen J.},
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KEYWORDS = {explicit network, from distances, identifiability, mrca network, phylogenetic network, phylogeny, reconstruction}
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106

@Article{Willson2007a,
AUTHOR = {Willson, Stephen J.},
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@Article{WuGusfield2007a,
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TITLE = {Efficient Computation of Minimum Recombination with Genotypes (not Haplotypes)},
YEAR = {2007},
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@Article{DFGP2006,
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@Article{MCDB2005,
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@Article{BeikoHamilton2006,
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@Article{GMZS2006,
AUTHOR = {Gupta, Arvind and Manuch, J{\~A}�n and Zhao, Xiaohong and Stacho, Ladislav},
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YEAR = {2006},
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JOURNAL = {Pattern Recognition},
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PAGES = {2312-2322},
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@Article{GBBS2007,
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@Article{KryukovSaitou2003,
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138

@Article{DHKM2008,
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YEAR = {2008},
JOURNAL = {EJC},
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NOTE = {http://www.ims.nus.edu.sg/preprints/2007-21.pdf},
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139

@Article{KloepperHuson2008,
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TITLE = {Drawing explicit phylogenetic networks and their integration into SplitsTree},
YEAR = {2008},
JOURNAL = {BMCEB},
VOLUME = {8},
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140

@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},
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NOTE = {http://dx.doi.org/10.1186/1471-2148-10-254},
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141

@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}
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142

@Article{LevyPachter2008,
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TITLE = {The Neighbor-Net Algorithm},
YEAR = {2011},
JOURNAL = {Advances in Applied Mathematics},
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URL = {http://dx.doi.org/10.1016/j.aam.2010.09.002},
NOTE = {http://arxiv.org/abs/math/0702515},
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143

@Article{IKLS2014,
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YEAR = {2014},
JOURNAL = {SIDMA},
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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}
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144

@Article{WPC2008,
AUTHOR = {Woolley, Steven M. and Posada, David and Crandall, Keith A.},
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YEAR = {2008},
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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}
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145

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AUTHOR = {Linz, Simone and Semple, Charles},
TITLE = {Hybridization in non-binary trees},
YEAR = {2009},
JOURNAL = {TCBB},
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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}
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147

@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},
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YEAR = {2006},
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@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},
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JOURNAL = {GEN},
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153

@Article{MSS2011,
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URL = {http://dx.doi.org/10.1145/2000807.2000810},
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ANNOTE = {BIBUPDATE : 20080605, http://www.cs.technion.ac.il/~moran/r/PS/TALG-20Nov2008.pdf},
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154

@Article{SnirTuller2009,
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TITLE = {The NET-HMM approach: Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models},
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JOURNAL = {JBCB},
VOLUME = {7},
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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}
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155

@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}
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TITLE = {Metrics for phylogenetic networks I: Generalizations of the Robinson-Foulds metric},
YEAR = {2009},
JOURNAL = {TCBB},
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@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},
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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},
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@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},
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URL = {http://dx.doi.org/10.1186/1471-2105-9-322},
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160

@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},
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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}
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161

@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},
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KEYWORDS = {explicit network, from unrooted trees, hybridization, lineage sorting, phylogenetic network, phylogeny, reconstruction, supernetwork}
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@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},
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KEYWORDS = {distance between networks, phylogenetic network, phylogeny}
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@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},
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KEYWORDS = {coalescent, evaluation, explicit network, galled tree, phylogenetic network, phylogeny, Program Recodon, regular network, simulation, tree sibling network, tree-child network}
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164

@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},
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@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},
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166

@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},
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167

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TITLE = {Recodon: Coalescent simulation of coding DNA sequences with recombination, migration and demography},
YEAR = {2008},
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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}
}

212

@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}
}

213

@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}
}

214

@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}
}

215

@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}
}

216

@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}
}

217

@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}
}

218

@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}
}

219

@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}
}

220

@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}
}

221

@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}
}

222

@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}
}

223

@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}
}

224

@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}
}

225

@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}
}

226

@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}
}

227

@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}
}

228

@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}
}

229

@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}
}

230

@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}
}

231

@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}
}

232

@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}
}

233

@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}
}

234

@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}
}

235

@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}
}

236

@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}
}

237

@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}
}

238

@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}
}

239

@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}
}

240

@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}
}

241

@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}
}

242

@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}
}

243

@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}
}

244

@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}
}

245

@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}
}

246

@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}
}

247

@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}
}

248

@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}
}

249

@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}
}

250

@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}
}

251

@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}
}

252

@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}
}

253

@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}
}

254

@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}
}

255

@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}
}

256

@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}
}

257

@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}
}

258

@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}
}

259

@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}
}

260

@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}
}

261

@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}
}

262

@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}
}

263

@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}
}

264

@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}
}

265

@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}
}

266

@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}
}

267

@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}
}

268

@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}
}

269

@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}
}

270

@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}
}

271

@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}
}

272

@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}
}

273

@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}
}

274

@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}
}

275

@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}
}

276

@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}
}

277

@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}
}

278

@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}
}

279

@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}
}

280

@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}
}

281

@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}
}

282

@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}
}

283

@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}
}

284

@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}
}

285

@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}
}

286

@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}
}

287

@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}
}

288

@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}
}

289

@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}
}

290

@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}
}

291

@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}
}

292

@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}
}

293

@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}
}

294

@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}
}

295

@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}
}

296

@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}
}

297

@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}
}

298

@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}
}

299

@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}
}

300

@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}
}

301

@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}
}

302

@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}
}

303

@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}
}

304

@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}
}

305

@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}
}

306

@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}
}

307

@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}
}

308

@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}
}

309

@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}
}

310

@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}
}

311

@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}
}

312

@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}
}

313

@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}
}

314

@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}
}

315

@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}
}

316

@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}
}

317

@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}
}

318

@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}
}

319

@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}
}

320

@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}
}

321

@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}
}

322

@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}
}

323

@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}
}

324

@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}
}

325

@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}
}

326

@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}
}

327

@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}
}

328

@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}
}

329

@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}
}

330

@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}
}

331

@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}
}

332

@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}
}

333

@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}
}

334

@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}
}

335

@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}
}

336

@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}
}

337

@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}
}

338

@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}
}

339

@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}
}

340

@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}
}

341

@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}
}

342

@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}
}

343

@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}
}

344

@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}
}

345

@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}
}

346

@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}
}

347

@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}
}

348

@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}
}

349

@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}
}

350

@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}
}

351

@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}
}

352

@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}
}

353

@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}
}

354

@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}
}

355

@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}
}

356

@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}
}

357

@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}
}

358

@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}
}

359

@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}
}

360

@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}
}

361

@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}
}

362

@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}
}

363

@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}
}

364

@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}
}

365

@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}
}

366

@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}
}

367

@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}
}

368

@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}
}

369

@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}
}

370

@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}
}

371

@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}
}

372

@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}
}

373

@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}
}

374

@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}
}

375

@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}
}

376

@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}
}

377

@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}
}

378

@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}
}

379

@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}
}

380

@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}
}

381

@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}
}

382

@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}
}

383

@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}
}

384

@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}
}

385

@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}
}

386

@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}
}

387

@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}
}

388

@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}
}

389

@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}
}

390

@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}
}

391

@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}
}

392

@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}
}

393

@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}
}

394

@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}
}

395

@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}
}

396

@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}
}

397

@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}
}

398

@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}
}

399

@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}
}

400

@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}
}

401

@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}
}

402

@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}
}

403

@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}
}

404

@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}
}

405

@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}
}

406

@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}
}

407

@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}
}

408

@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}
}

409

@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}
}

410

@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}
}

411

@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}
}

412

@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}
}

413

@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}
}

414

@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}
}

415

@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}
}

416

@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}
}

417

@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}
}

418

@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}
}

419

@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}
}

420

@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}
}

421

@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}
}

422

@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}
}

423

@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}
}

424

@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}
}

425

@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}
}

426

@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}
}

427

@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}
}

428

@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}
}

429

@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}
}

430

@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}
}

431

@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}
}

432

@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}
}

433

@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}
}

434

@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}
}

435

@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}
}

436

@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}
}

437

@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}
}

438

@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}
}

439

@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}
}

440

@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}
}

441

@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}
}

442

@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}
}

443

@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}
}

444

@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}
}

445

@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}
}

446

@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}
}

447

@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}
}

448

@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}
}

449

@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}
}

450

@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}
}

451

@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}
}

452

@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}
}

InProceedings

1

@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

@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}
}

3

@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 : }
}

4

@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}
}

5

@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}
}

6

@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}
}

7

@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}
}

8

@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}
}

9

@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}
}

10

@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 : }
}

11

@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}
}

12

@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 : }
}

13

@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}
}

14

@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}
}

15

@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}
}

16

@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}
}

17

@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}
}

18

@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}
}

19

@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}
}

20

@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}
}

21

@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}
}

22

@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}
}

23

@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}
}

24

@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}
}

25

@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}
}

26

@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}
}

27

@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}
}

28

@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}
}

29

@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}
}

30

@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}
}

31

@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}
}

32

@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}
}

33

@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}
}

34

@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}
}

35

@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}
}

36

@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}
}

37

@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}
}

38

@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}
}

39

@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}
}

40

@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}
}

41

@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}
}

42

@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}
}

43

@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}
}

44

@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}
}

45

@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}
}

46

@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}
}

47

@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}
}

48

@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}
}

49

@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}
}

50

@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}
}

51

@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}
}

52

@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}
}

53

@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}
}

54

@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}
}

55

@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}
}

56

@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}
}

57

@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}
}

58

@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}
}

59

@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}
}

60

@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}
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61

@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}
}

62

@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}
}

63

@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}
}

64

@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}
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65

@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}
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66

@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}
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67

@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}
}

68

@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}
}

69

@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}
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70

@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},
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71

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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},
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KEYWORDS = {bootstrap, explicit network, from rooted trees, from sequences, lateral gene transfer, phylogenetic network, phylogeny, Program Nepal, Program PhyloNet, reconstruction}
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72

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YEAR = {2005},
BOOKTITLE = {Proceedings of the Second International Conference on Distributed Computing and Internet Technology (ICDCIT'05)},
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PAGES = {316-325},
URL = {http://dx.doi.org/10.1145/974614.974656},
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ANNOTE = {CITE : },
KEYWORDS = {duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction}
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74

@InProceedings{Gorecki2003,
AUTHOR = {G{\~A}�recki, Pawel},
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BOOKTITLE = {ECCB03},
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ANNOTE = {BIBUPDATE : 20081127},
KEYWORDS = {duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction}
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76

@InProceedings{ToHabib2009,
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YEAR = {2009},
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AUTHOR = {Gambette, Philippe and Berry, Vincent and Paul, Christophe},
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YEAR = {2009},
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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/},
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78

@InProceedings{HRBGP2009,
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BOOKTITLE = {ISMBECCB09},
VOLUME = {25},
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YEAR = {2004},
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YEAR = {2006},
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SERIES = {Studies in Classification, Data Analysis, and Knowledge Organization},
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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}
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AUTHOR = {Asano, Tetsuo and Jansson, Jesper and Sadakane, Kunihiko and Uehara, Ryuhei and Valiente, Gabriel},
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YEAR = {2010},
BOOKTITLE = {CPM10},
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SERIES = {LNCS},
PUBLISHER = {springer},
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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}
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87

@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}
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88

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AUTHOR = {Wu, Yufeng and Wang, Jiayin},
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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}
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89

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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}
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90

@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}
}

91

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AUTHOR = {Park, Hyun Jung and Jin, Guohua and Nakhleh, Luay},
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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}
}

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KEYWORDS = {abstract network, from quartets, phylogenetic network, phylogeny, polynomial, Program SplitsTree, reconstruction, split network, weakly compatible}
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AUTHOR = {Bandelt, Hans-J{\~A}�rgen and Dress, Andreas W. M.},
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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}
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AUTHOR = {Whidden, Chris and Beiko, Robert G. and Zeh, Norbert},
TITLE = {Fast FPT Algorithms for Computing Rooted Agreement Forests: Theory and Experiments},
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VOLUME = {6049},
PAGES = {141-153},
SERIES = {LNCS},
PUBLISHER = {springer},
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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}
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95

@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}
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NOTE = {http://safrabio.cs.tau.ac.il/download/Papers/Birin_et_al.pdf},
KEYWORDS = {explicit network, from sequences, phylogenetic network, phylogeny, reconstruction}
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@InProceedings{ParkNakhleh2012,
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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}
}

99

@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}
}

100

@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}
}

101

@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}
}

102

@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}
}

103

@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}
}

104

@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}
}

105

@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}
}

106

@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}
}

107

@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}
}

108

@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}
}

109

@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}
}

110

@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}
}

111

@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}
}

112

@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}
}

113

@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}
}

114

@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}
}

115

@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}
}

116

@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}
}

117

@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}
}

118

@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}
}

119

@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}
}

120

@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}
}

121

@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}
}

122

@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}
}

123

@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}
}

124

@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}
}

125

@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}
}

126

@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}
}

127

@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}
}

128

@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}
}

129

@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}
}

130

@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}
}

131

@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}
}

132

@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}
}

133

@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}
}

134

@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}
}

135

@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}
}

136

@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}
}

137

@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}
}

138

@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}
}

139

@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}
}

140

@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}
}

141

@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}
}

142

@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}
}

143

@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}
}

144

@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}
}

145

@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}
}

146

@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}
}

147

@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}
}

148

@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}
}

149

@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}
}

150

@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}
}

151

@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}
}

152

@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}
}

153

@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}
}

InBook

1

@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 : }
}

2

@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}
}

3

@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}
}

4

@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}
}

5

@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}
}

6

@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}
}

7

@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}
}

8

@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}
}

9

@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}
}

10

@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}
}

11

@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}
}

12

@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}
}

13

@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}
}

14

@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}
}

15

@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}
}

16

@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}
}

17

@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}
}

18

@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}
}

19

@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}
}

20

@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}
}

21

@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}
}

22

@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}
}

23

@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}
}

24

@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}
}

25

@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}
}

26

@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}
}

27

@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}
}

28

@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}
}

29

@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}
}

30

@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}
}

31

@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}
}

MastersThesis

1

@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}
}

2

@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}
}

3

@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}
}

4

@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}
}

5

@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}
}

6

@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}
}

7

@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}
}

8

@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}
}

9

@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}
}

10

@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}
}

11

@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}
}

12

@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}
}

13

@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}
}

14

@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}
}

PhdThesis

1

@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

@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 : }
}

3

@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

@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}
}

5

@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}
}

6

@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}
}

7

@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}
}

8

@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}
}

9

@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}
}

10

@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}
}

11

@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}
}

12

@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}
}

13

@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}
}

14

@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}
}

15

@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}
}

16

@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}
}

17

@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}
}

18

@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}
}

19

@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}
}

20

@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}
}

21

@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}
}

22

@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}
}

23

@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}
}

24

@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}
}

25

@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}
}

26

@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}
}

27

@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}
}

28

@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}
}

29

@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}
}

30

@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}
}

31

@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}
}

32

@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}
}

33

@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}
}

34

@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}
}

35

@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}
}

36

@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}
}

37

@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}
}

38

@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}
}

39

@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}
}

40

@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}
}

41

@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/}
}

42

@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}
}

43

@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}
}

44

@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}
}

45

@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}
}

46

@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}
}

47

@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}
}

48

@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}
}

49

@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}
}

50

@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}
}

51

@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}
}

52

@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}
}

53

@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}
}

54

@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}
}

55

@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}
}

Misc

1

@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}
}

2

@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}
}

3

@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}
}

4

@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 : }
}

5

@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}
}

6

@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}
}

7

@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}
}

8

@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}
}

9

@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}
}

10

@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}
}

11

@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}
}

12

@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}
}

13

@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}
}

14

@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}
}

15

@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}
}

16

@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}
}

17

@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}
}

18

@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}
}

19

@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}
}

20

@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}
}

21

@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}
}

22

@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}
}

23

@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}
}

24

@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}
}

25

@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}
}

26

@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}
}

27

@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}
}

28

@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}
}

29

@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}
}

30

@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}
}

31

@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}
}

32

@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}
}

33

@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}
}

34

@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}
}

35

@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}
}

36

@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}
}

37

@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}
}

38

@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}
}

39

@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}
}

40

@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}
}

41

@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}
}

42

@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}
}

43

@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}
}

Book

1

@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}
}

2

@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}
}

3

@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}
}

4

@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}
}

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