Who is Who in Phylogenetic Networks

Publications of Year 2020

Article (Journal)

1 Katharina Huber and Guillaume Scholz. Phylogenetic networks that are their own fold-ups. In AAM, Vol. 113(101959):1-24, 2020. Keywords: characterization, explicit network, FU-stable network, phylogenetic network, phylogeny. Note: https://arxiv.org/abs/1804.01841.         2 Leo van Iersel, Vincent Moulton and Yukihiro Murakami. Reconstructibility of unrooted level-k phylogenetic networks from distances. In AAM, Vol. 120(102075):1-30, 2020. Keywords: from distances, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction, uniqueness. Note: https://doi.org/10.1016/j.aam.2020.102075.         3 Andreas Gunawan, Jeyaram Rathin and Louxin Zhang. Counting and enumerating galled networks. In DAM, Vol. 283:644-654, 2020. Keywords: counting, enumeration, explicit network, galled network, phylogenetic network, phylogeny. Note: https://arxiv.org/abs/1812.08569.         4 Jonathan Klawitter. The agreement distance of unrooted phylogenetic networks. In DMTCS, Vol. 21(2):22.1-23, 2020. Keywords: agreement forest, distance between networks, explicit network, from network, phylogenetic network, phylogeny. Note: https://dmtcs.episciences.org/6567/pdf.         5 Momoko Hayamizu, Katharina Huber, Vincent Moulton and Yukihiro Murakami. Recognizing and realizing cactus metrics. In IPL, Vol. 157(105916):1-5, 2020. Keywords: cactus graph, from distances, level k phylogenetic network, optimal realization, polynomial. Note: https://doi.org/10.1016/j.ipl.2020.105916.         6 Gabriel Cardona and Louxin Zhang. Counting and Enumerating Tree-Child Networks and Their Subclasses. In JCSS, Vol. 114:84-104, 2020. Keywords: counting, enumeration, explicit network, galled network, galled tree, normal network, phylogenetic network, phylogeny, tree-child network.         7 Mathilde Bouvel, Philippe Gambette and Marefatollah Mansouri. Counting Phylogenetic Networks of Level 1 and 2. In JOMB, 2020. Keywords: counting, explicit network, level k phylogenetic network, phylogenetic network, phylogeny. Note: https://arxiv.org/abs/1909.10460, to appear.         8 Simone Linz and Charles Semple. Caterpillars on three and four leaves are sufficient to reconstruct binary normal networks. In JOMB, 2020. Keywords: explicit network, from rooted trees, from triplets, normal network, phylogenetic network, phylogeny, reconstruction, uniqueness. Note: https://arxiv.org/abs/2002.00483, to appear.         9 Cassandra Durell and Stefan Forcey. Level-1 phylogenetic networks and their balanced minimum evolution polytopes. In JOMB, Vol. 80:1235-1263, 2020. Keywords: from distances, galled tree, phylogenetic network, phylogeny, reconstruction, split network. Note: https://arxiv.org/pdf/1905.09160.pdf.         10 Hadi Poormohammadi, Mohsen Sardari Zarchi and Hossein Ghaneai. NCHB: A method for constructing rooted phylogenetic networks from rooted triplets based on height function and binarization. In JTB, Vol. 489(110144), 2020. Keywords: explicit network, from triplets, heuristic, phylogenetic network, phylogeny, Program Simplistic, Program TripNet, reconstruction. Note: https://doi.org/10.1016/j.jtbi.2019.110144.         11 Hadi Poormohammadi and Mohsen Sardari Zarchi. Netcombin: An algorithm for constructing optimal phylogenetic network from rooted triplets. In PLoS ONE, Vol. 15(9):e0227842.1-25, 2020. Keywords: explicit network, from triplets, heuristic, phylogenetic network, phylogeny, Program Simplistic, Program TripNet, reconstruction. Note: https://doi.org/10.1371/journal.pone.0227842.         12 Leo van Iersel, Remie Janssen, Mark Jones, Yukihiro Murakami and Norbert Zeh. Polynomial-Time Algorithms for Phylogenetic Inference Problems Involving Duplication and Reticulation. In TCBB, Vol. 17(1):14-26, 2020. Keywords: hybridization, minimum number, parental hybridization, phylogenetic network, phylogeny, reconstruction, weakly displaying. Note: http://pure.tudelft.nl/ws/portalfiles/portal/71270795/08798653.pdf.         13 Joan Carles Pons, Celine Scornavacca and Gabriel Cardona. Generation of Level-k LGT Networks. In TCBB, Vol. 17(1):158-164, 2020. Keywords: explicit network, level k phylogenetic network, LGT network, phylogenetic network, phylogeny.

InProceedings

14 Remie Janssen, Mark Jones and Yukihiro Murakami. Combining Networks Using Cherry Picking Sequences. In AlCoB20, Vol. 12099:77-92 of LNCS, Springer, 2020. Keywords: cherry-picking, explicit network, FPT, from network, hybridization, orchard network, phylogenetic network, phylogeny, tree-child network.         15 Remie Janssen and Yukihiro Murakami. Linear Time Algorithm for Tree-Child Network Containment. In AlCoB20, Vol. 12099:93-107 of LNCS, Springer, 2020. Keywords: explicit network, from network, isomorphism, phylogenetic network, phylogeny, polynomial, reconstruction, tree-child network, tree-child sequence. Note: https://doi.org/10.1007/978-3-030-42266-0_8.         16 Hannah Brown, Lei Zuo and Dan Gusfield. Comparing Integer Linear Programming to SAT-Solving for Hard Problems in Computational and Systems Biology. In AlCoB2020, Vol. 12099:63-76 of LNCS, Springer, 2020. Keywords: from binary characters, History bound, integer linear programming, minimum number, phylogeny, SAT. Note: https://doi.org/10.1007/978-3-030-42266-0_6.         17 Louxin Zhang. Recent Progresses in the Combinatorial and Algorithmic Study of Rooted Phylogenetic Networks. In WALCOM20, Vol. 12049:22-27 of LNCS, Springer, 2020. Keywords: cluster containment, galled network, galled tree, nearly-stable network, phylogenetic network, phylogeny, polynomial, reticulation-visible network, survey, time consistent network, tree containment, tree-based network, tree-child network.

PhdThesis

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

Misc

19 Andrew R. Francis, Daniel H. Huson and Mike Steel. Normalising phylogenetic networks. 2020. Keywords: explicit network, from network, normal network, phylogenetic network, phylogeny, polynomial, Program PhyloSketch, reconstruction, tree-child network. Note: https://arxiv.org/abs/2008.07797.         20 Michael Fuchs, Guan-Ru Yu and Louxin Zhang. On the Asymptotic Growth of the Number of Tree-Child Networks. 2020. Keywords: counting, explicit network, phylogenetic network, phylogeny, tree-child network. Note: https://arxiv.org/abs/2003.08049.         21 Marefatollah Mansouri. Counting General Phylogenetic networks. 2020. Keywords: counting, explicit network, phylogenetic network, phylogeny. Note: https://arxiv.org/abs/2005.14547.         22 Jonathan Klawitter and Peter Stumpf. Drawing Tree-Based Phylogenetic Networks with Minimum Number of Crossings. 2020. Keywords: explicit network, FPT, minimum number, NP complete, phylogenetic network, phylogeny, polynomial, visualization. Note: https://arxiv.org/abs/2008.08960.         23 Elizabeth Gross, Leo van Iersel, Remie Janssen, Mark Jones, Colby Long and Yukihiro Murakami. Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes. 2020. Keywords: characterization, distinguishability, explicit network, galled tree, phylogenetic network, population genetics, semidirected network, statistical model, uniqueness. Note: https://arxiv.org/abs/2007.08782.         24 Stefan Forcey and Drew Scalzo. Phylogenetic networks as circuits with resistance distance. 2020. Keywords: circular split system, from distances, level k phylogenetic network, NeighborNet, nested network, phylogenetic network, phylogeny, split network. Note: https://arxiv.org/abs/2007.13574.         25 Stefan Forcey and Drew Scalzo. Galois connections for phylogenetic networks and their polytopes. 2020. Keywords: characterization, from distances, galled tree, planar, reconstruction, split network. Note: https://arxiv.org/abs/2004.11944.         26 Katharina Huber, Simone Linz and Vincent Moulton. Weakly displaying trees in temporal tree-child network. 2020. Keywords: cherry-picking, from rooted trees, phylogenetic network, phylogeny, reconstruction, rigidly displaying, time consistent network, tree-child network, weakly displaying. Note: https://arxiv.org/abs/2004.02634.