Search results for ' Algorithms for Molecular Biology ' :
    500 matches found.
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Alberto Apostolico, Matteo Comin, Andreas W. M. Dress and Laxmi Parida. Ultrametric networks: a new tool for phylogenetic analysis. In Algorithms for Molecular Biology, Vol. 8(7):1-10, 2013.  
Keywords: abstract network, from distances, phylogenetic network, phylogeny, Program Ultranet.
Note: http://dx.doi.org/10.1186/1748-7188-8-7.
       
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Gabriel Cardona, Francesc Rosselló and Gabriel Valiente. Extended Newick: It is Time for a Standard Representation. In BMCB, Vol. 9:532, 2008.  
Keywords: evaluation, explicit network, phylogenetic network, Program Bio PhyloNetwork, Program Dendroscope, Program NetGen, Program PhyloNet, Program SplitsTree, Program TCS, visualization.
Note: http://bioinfo.uib.es/media/uploaded/bmc-2008-enewick-sub.pdf.
       

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

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Jialiang Yang, Stefan Grünewald, Yifei Xu and Xiu-Feng Wan. Quartet-based methods to reconstruct phylogenetic networks. In BMC Systems Biology, Vol. 80(21), 2014.  
Keywords: abstract network, from quartets, phylogenetic network, phylogeny, Program QuartetMethods, Program QuartetNet, Program SplitsTree, reconstruction.
Note: http://dx.doi.org/10.1186/1752-0509-8-21 .
       
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Monika Balvociute, Andreas Spillner and Vincent Moulton. FlatNJ: A Novel Network-Based Approach to Visualize Evolutionary and Biogeographical Relationships. In Systematic Biology, Vol. 63(3):383-396, 2014.  
Keywords: abstract network, flat, phylogenetic network, phylogeny, Program FlatNJ, Program SplitsTree, split network.
Note: http://dx.doi.org/10.1093/sysbio/syu001.
       
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Joel Sjöstrand, Ali Tofigh, Vincent Daubin, Lars Arvestad, Bengt Sennblad and Jens Lagergren. A Bayesian Method for Analyzing Lateral Gene Transfer. In Systematic Biology, Vol. 63(3):409-420, 2014.  
Keywords: bayesian, duplication, from rooted trees, from sequences, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program JPrIME-DLTRS, reconstruction.
Note: http://dx.doi.org/10.1093/sysbio/syu007.
       

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Robert G. Beiko. Gene sharing and genome evolution: networks in trees and trees in networks. In Biology and Philosophy, Vol. 25(4):659-673, 2010.  
Keywords: abstract network, explicit network, from rooted trees, galled network, phylogenetic network, phylogeny, Program Dendroscope, Program SplitsTree, reconstruction, split network, survey.
Note: http://dx.doi.org/10.1007/s10539-010-9217-3.
       
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Steven M. Woolley, David Posada and Keith A. Crandall. A Comparison of Phylogenetic Network Methods Using Computer Simulation. In PLoS ONE, Vol. 3(4):e1913, 2008.  
Keywords: abstract network, distance between networks, evaluation, median network, MedianJoining, minimum spanning network, NeighborNet, parsimony, phylogenetic network, phylogeny, Program Arlequin, Program CombineTrees, Program Network, Program SHRUB, Program SplitsTree, Program TCS, split decomposition.
Note: http://dx.doi.org/10.1371/journal.pone.0001913.
       
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James B. Whitfield, Sydney A. Cameron, Daniel H. Huson and Mike Steel. Filtered Z-Closure Supernetworks for Extracting and Visualizing Recurrent Signal from Incongruent Gene Trees. In Systematic Biology, Vol. 57(6):939-947, 2008.  
Keywords: abstract network, from unrooted trees, phylogenetic network, phylogeny, Program SplitsTree, split, split network, supernetwork.
Note: http://www.life.uiuc.edu/scameron/pdfs/Filtered%20Z-closure%20SystBiol.pdf.
       

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Tobias Kloepper. Algorithms for the Calculation and Visualisation of Phylogenetic Networks. PhD thesis, Eberhard-Karls-Universität Tübingen, Germany, 2008.  
Keywords: from rooted trees, from sequences, from unrooted trees, galled network, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network, visualization.
Note: https://publikationen.uni-tuebingen.de/xmlui/handle/10900/49159.
       

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Tamir Tuller and Sagi Snir. The NET-HMM: a HMM Based Likelihood Model for Evolutionary Networks. 2007.  
Keywords: lateral gene transfer, likelihood, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: Poster presented at the eleventh Annual International Conference on Research in Computational Molecular Biology (RECOMB'07), http://www.qb3.org/recomb07/posters/Tuller013043013RECOMB_HMM1.pdf.
       

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Sergey Bereg and Kathryn Bean. Constructing Phylogenetic Networks from Trees. In BIBE05, Pages 299-305, 2005. 1 comment  
Keywords: evaluation, from distances, phylogenetic network, phylogeny, Program SplitsTree, Program T REX, reconstruction, split, split network.
Note: http://dx.doi.org/10.1109/BIBE.2005.19.
       
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David A. Morrison. Networks in phylogenetic analysis: new tools for population biology. In IJP, Vol. 35:567-582, 2005.  
Keywords: median network, NeighborNet, phylogenetic network, phylogeny, population genetics, Program Network, Program Spectronet, Program SplitsTree, Program T REX, Program TCS, reconstruction, reticulogram, split decomposition, survey.
Note: http://hem.fyristorg.com/acacia/papers/networks.pdf.
       

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Insa Cassens, Patrick Mardulyn and Michel C. Milinkovitch. Evaluating Intraspecific Network Construction Methods Using Simulated Sequence Data: Do Existing Algorithms Outperform the Global Maximum Parsimony Approach? In Systematic Biology, Vol. 54(3):363-372, 2005.  
Keywords: abstract network, evaluation, from unrooted trees, haplotype network, parsimony, phylogenetic network, phylogeny, Program Arlequin, Program CombineTrees, Program Network, Program TCS, reconstruction, software.
Note: http://www.lanevol.org/LANE/publications_files/Cassens_etal_SystBio_2005.pdf.
       

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Mohd Abdul Hai Zahid, Ankush Mittal and Ramesh C. Joshi. Use of Phylogenetic network and its reconstruction Algorithms. In Bioinformatics India, Vol. 2:47-58, 2004.  
Keywords: evaluation, from distances, NeighborNet, Program SplitsTree, Program T REX, split decomposition.
Note: http://www.isical.ac.in/~zahid_t/publications/papers/1.pdf.
       

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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.
       

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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.
       

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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Leo van Iersel, Steven Kelk, Nela Lekic and Leen Stougie. Approximation algorithms for nonbinary agreement forests. In SIDMA, Vol. 28(1):49-66, 2014.  
Keywords: agreement forest, approximation, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1210.3211.
       
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Jesper Jansson and Andrzej Lingas. Computing the rooted triplet distance between galled trees by counting triangles. In Journal of Discrete Algorithms, Vol. 25:66-78, 2014.  
Keywords: distance between networks, explicit network, from network, galled network, phylogenetic network, phylogeny, polynomial, triplet distance.
       
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David A. Morrison. Next generation sequencing and phylogenetic networks. In EMBnet.journal, Vol. 20(e760):1-4, 2014.  
Keywords: abstract network, from NGS data, phylogenetic network, phylogeny, Program SplitsTree, reconstruction.
       

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Juan Wang. A new algorithm to construct phylogenetic networks from trees. In Genetics and Molecular Research, Vol. 13(1):1456-1464, 2014.  
Keywords: explicit network, from clusters, heuristic, phylogenetic network, Program LNetwork, Program QuickCass, reconstruction.
Note: http://dx.doi.org/10.4238/2014.March.6.4.
       
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David A. Morrison. Is the Tree of Life the Best Metaphor, Model, or Heuristic for Phylogenetics? In Systematic Biology, Vol. 63(4):628-638, 2014.  
Keywords: abstract network, explicit network, phylogenetic network, phylogeny, survey.
       

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Chris Whidden, Robert G. Beiko and Norbert Zeh. Fixed-Parameter Algorithms for Maximum Agreement Forests. In SICOMP, Vol. 42(4):1431-1466, 2013.  
Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, SPR distance.
Note: http://arxiv.org/abs/1108.2664, slides.
       
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Stefan Grünewald, Andreas Spillner, Sarah Bastkowski, Anja Bögershausen and Vincent Moulton. SuperQ: Computing Supernetworks from Quartets. In TCBB, Vol. 10(1):151-160, 2013.  
Keywords: abstract network, circular split system, from quartets, heuristic, phylogenetic network, phylogeny, Program QNet, Program SplitsTree, Program SuperQ, software, split network.
       
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Yun Yu, R. Matthew Barnett and Luay Nakhleh. Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting. In Systematic Biology, Vol. 62(5):738-751, 2013.  
Keywords: from network, from rooted trees, hybridization, lineage sorting, parsimony, phylogenetic network, phylogeny, Program PhyloNet, reconstruction.
       
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Alexey A. Morozov, Yuri P. Galachyants and Yelena V. Likhoshway. Inferring Phylogenetic Networks from Gene Order Data. In BMRI, Vol. 2013(503193):1-7, 2013.  
Keywords: abstract network, from distances, from gene order, NeighborNet, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split decomposition, split network.
       
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Leo van Iersel, Steven Kelk, Nela Lekic and Leen Stougie. A short note on exponential-time algorithms for hybridization number. 2013.  
Keywords: explicit network, exponential algorithm, from rooted trees, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1312.1255.
       

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

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Gergely J. Szöllösi, Eric Tannier, Nicolas Lartillot and Vincent Daubin. Lateral Gene Transfer from the Dead. In Systematic Biology, Vol. 62(3):386-397, 2013.  
Keywords: duplication, lateral gene transfer, likelihood, loss, phylogeny, Program TERA, reconstruction.
Note: http://dx.doi.org/10.1093/sysbio/syt003.
       
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Sarah Bastkowski. From Trees to Networks and Back. PhD thesis, University of East Anglia, 2013.  
Keywords: abstract network, NeighborNet, phylogenetic network, phylogeny, Program FlatNJ, Program QNet, Program SplitsTree, reconstruction, software, split network.
Note: http://spectre-suite-of-phylogenetic-tools-for-reticulate-evolution.readthedocs.io/en/latest/_downloads/spectre_bastkowskis_thesis.pdf.
       

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

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Andreas Spillner and Vincent Moulton. Optimal algorithms for computing edge weights in planar split-networks. In Journal of Applied Mathematics and Computing, Vol. 39(1-2):1-13, 2012.  
Keywords: abstract network, from distances, phylogenetic network, phylogeny, reconstruction, split, split network.
Note: http://dx.doi.org/10.1007/s12190-011-0506-z.
       
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Zhi-Zhong Chen and Lusheng Wang. Algorithms for Reticulate Networks of Multiple Phylogenetic Trees. In TCBB, Vol. 9(2):372-384, 2012.  
Keywords: explicit network, from rooted trees, minimum number, phylogenetic network, phylogeny, Program CMPT, Program MaafB, reconstruction, software.
Note: http://rnc.r.dendai.ac.jp/~chen/papers/rMaaf.pdf.
       
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Changiz Eslahchi, Reza Hassanzadeh, Ehsan Mottaghi, Mahnaz Habibi, Hamid Pezeshk and Mehdi Sadeghi. Constructing circular phylogenetic networks from weighted quartets using simulated annealing. In MBIO, Vol. 235(2):123-127, 2012.  
Keywords: abstract network, from quartets, heuristic, phylogenetic network, phylogeny, Program SAQ-Net, Program SplitsTree, reconstruction, simulated annealing, software, split network.
Note: http://dx.doi.org/10.1016/j.mbs.2011.11.003.
       
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Mukul S. Bansal, Eric J. Alm and Manolis Kellis. Efficient Algorithms for the Reconciliation Problem with Gene Duplication, Horizontal Transfer, and Loss. In ISMB12, Vol. 28(12):i283-i291 of BIO, 2012.  
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program Angst, Program Mowgli, Program RANGER-DTL, reconstruction.
Note: http://dx.doi.org/10.1093/bioinformatics/bts225.
       
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Daniel H. Huson and Celine Scornavacca. Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks. In Systematic Biology, Vol. 61(6):1061-1067, 2012.  
Keywords: from rooted trees, from triplets, phylogenetic network, phylogeny, Program Dendroscope, reconstruction, software, visualization.
       
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Adrià Alcalà Mena and Francesc Rosselló. Ternary graph isomorphism in polynomial time, after Luks. 2012.  
Keywords: distance between networks, explicit network, from network, isomorphism, phylogenetic network, phylogeny, polynomial, Program SAGE.
Note: http://arxiv.org/abs/1209.0871.
       

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

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Daniel H. Huson and Celine Scornavacca. A survey of combinatorial methods for phylogenetic networks. In Genome Biology and Evolution, Vol. 3:23-35, 2011.  
Keywords: phylogenetic network, survey.
Note: http://dx.doi.org/10.1093/gbe/evq077.
       
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Daniel H. Huson, Regula Rupp and Celine Scornavacca. Phylogenetic Networks: Concepts, Algorithms and Applications. Cambridge University Press, 2011.  
Keywords: phylogenetic network, phylogeny, survey.
Note: http://www.phylogenetic-networks.org/, buy at Amazon.com. Reviews here and there.
       

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Gergely J. Szöllösi and Vincent Daubin. Modeling Gene Family Evolution and Reconciling Phylogenetic Discord. In Evolutionary Genomics, Statistical and Computational Methods, Volume 2, Methods in Molecular Biology, Vol. 856:29-51, Chapter 2, springer, 2011.  
Keywords: duplication, from multilabeled tree, lateral gene transfer, likelihood, phylogeny, reconstruction, statistical model.
Note: ArXiv version entitled The pattern and process of gene family evolution.
       
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Jean-Philippe Doyon, Vincent Ranwez, Vincent Daubin and Vincent Berry. Models, algorithms and programs for phylogeny reconciliation. In Briefings in Bioinformatics, Vol. 12(5):392-400, 2011.  
Keywords: explicit network, lateral gene transfer, phylogenetic network, phylogeny, reconstruction, survey.
       
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Jaroslaw Byrka, Pawel Gawrychowski, Katharina Huber and Steven Kelk. Worst-case optimal approximation algorithms for maximizing triplet consistency within phylogenetic networks. In Journal of Discrete Algorithms, Vol. 8(1):65-75, 2010.  
Keywords: approximation, explicit network, from triplets, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/0710.3258.
       
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Changiz Eslahchi, Mahnaz Habibi, Reza Hassanzadeh and Ehsan Mottaghi. MC-Net: a method for the construction of phylogenetic networks based on the Monte-Carlo method. In BMCEB, Vol. 10:254, 2010.  
Keywords: abstract network, circular split system, from distances, heuristic, phylogenetic network, Program MC-Net, Program SplitsTree, software, split, split network.
Note: http://dx.doi.org/10.1186/1471-2148-10-254.
       
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Luay Nakhleh. Evolutionary phylogenetic networks: models and issues. In L. Heath and N. Ramakrishnan editors, The Problem Solving Handbook for Computational Biology and Bioinformatics, Springer, 2010.  
Keywords: phylogenetic network, phylogeny, survey.
Note: http://www.cs.rice.edu/~nakhleh/Papers/HeathRamakrishnanBookChapter.pdf.
       

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Joel Velasco and Elliott Sober. Testing for Treeness: Lateral Gene Transfer, Phylogenetic Inference, and Model Selection. In Biology and Philosophy, Vol. 25(4):675-687, 2010.  
Keywords: explicit network, model selection, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: http://joelvelasco.net/Papers/velascosober-testingfortreeness.pdf.
       
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David A. Morrison. Using data-display networks for exploratory data analysis in phylogenetic studies. In MBE, Vol. 27(5):1044-1057, 2010.  
Keywords: abstract network, hybridization, NeighborNet, Program SplitsTree, recombination, split decomposition.
Note: http://dx.doi.org/10.1093/molbev/msp309.
       
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Chris Whidden, Robert G. Beiko and Norbert Zeh. Fast FPT Algorithms for Computing Rooted Agreement Forests: Theory and Experiments. In Proceedings of the ninth International Symposium on Experimental Algorithms (SEA'10), Vol. 6049:141-153 of LNCS, springer, 2010.  
Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, SPR distance.
Note: https://www.cs.dal.ca/sites/default/files/technical_reports/CS-2010-03.pdf.
       
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Gabriel Cardona, Francesc Rosselló and Gabriel Valiente. Comparison of tree-child phylogenetic networks. In TCBB, Vol. 6(4):552-569, 2009.  
Keywords: explicit network, phylogenetic network, phylogeny, Program Bio PhyloNetwork, Program PhyloNetwork, tree sibling network, tree-child network.
Note: http://arxiv.org/abs/0708.3499.
       
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Daniel H. Huson. Drawing Rooted Phylogenetic Networks. In TCBB, Vol. 6(1):103-109, 2009.  
Keywords: explicit network, phylogenetic network, phylogeny, Program Dendroscope, Program SplitsTree, visualization.
Note: http://dx.doi.org/10.1109/TCBB.2008.58.
       
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Robert G. Beiko and Mark A. Ragan. Untangling Hybrid Phylogenetic Signals: Horizontal Gene Transfer and Artifacts of Phylogenetic Reconstruction. In Horizontal Gene Transfer, Vol. 532:241-256 of Methods in Molecular Biology, 2009.  
Note: http://dx.doi.org/10.1007/978-1-60327-853-9_14.
       
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Maria S. Poptsova. Testing Phylogenetic Methods to Identify Horizontal Gene Transfer. In Horizontal Gene Transfer, Pages 227-240, 2009.  
Note: http://dx.doi.org/10.1007/978-1-60327-853-9_13.
       
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Josh Voorkamp né Collins. Rekernelisation Algorithms in Hybrid Phylogenies. Master's thesis, University of Canterbury, New Zealand, 2009.  
Keywords: agreement forest, explicit network, FPT, from rooted trees, from unrooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, software.
Note: http://hdl.handle.net/10092/2852.
       

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Mark A. Ragan. Trees and networks before and after Darwin. In Biology Direct, Vol. 4(43), 2009.  
Keywords: abstract network, explicit network, phylogenetic network, phylogeny, survey, visualization.
Note: http://dx.doi.org/10.1186/1745-6150-4-43.
       
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Gabriel Valiente. Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R. Pages 184-208, Taylor & Francis/CRC Press, 2009.  
Keywords: counting, distance between networks, galled tree, generation, phylogenetic network, phylogeny, survey, time consistent network, tree sibling network, tree-child network.
Note: http://books.google.fr/books?id=F4YIIUWb7yMC.
       

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Laura S. Kubatko. Identifying Hybridization Events in the Presence of Coalescence via Model Selection. In Systematic Biology, Vol. 58(5):478-488, 2009.  
Keywords: AIC, BIC, branch length, coalescent, explicit network, from rooted trees, from species tree, hybridization, lineage sorting, model selection, phylogenetic network, phylogeny, statistical model.
Note: http://dx.doi.org/10.1093/sysbio/syp055.
       

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Bui Quang Minh, Steffen Klaere and Arndt von Haeseler. Taxon Selection under Split Diversity. In Systematic Biology, Vol. 58(6):586-594, 2009.  
Keywords: abstract network, circular split system, diversity, from network, phylogenetic network, split network.
Note: http://dx.doi.org/10.1093/sysbio/syp058.
       
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Vincent Moulton and Katharina Huber. Split Networks. A tool for exploring complex evolutionary relationships in molecular data. In Philippe Lemey, Marco Salemi and Anne-Mieke Vandamme editors, The Phylogenetic Handbook, Cambridge University Press, 2009.  
Keywords: abstract network, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network.
       

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Gabriel Cardona, Francesc Rosselló and Gabriel Valiente. Tripartitions do not always discriminate phylogenetic networks. In MBIO, Vol. 211(2):356-370, 2008.  
Keywords: distance between networks, phylogenetic network, phylogeny, Program Bio PhyloNetwork, tree-child network, tripartition distance.
Note: http://arxiv.org/abs/0707.2376, slides available at http://www.newton.cam.ac.uk/webseminars/pg+ws/2007/plg/plgw01/0904/valiente/.
       
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Philippe Gambette and Daniel H. Huson. Improved Layout of Phylogenetic Networks. In TCBB, Vol. 5(3):472-479, 2008.  
Keywords: abstract network, heuristic, phylogenetic network, phylogeny, Program SplitsTree, software, split network, visualization.
Note: http://hal-lirmm.ccsd.cnrs.fr/lirmm-00309694/en/.
       
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Gabriel Cardona, Francesc Rosselló and Gabriel Valiente. A Perl Package and an Alignment Tool for Phylogenetic Networks. In BMCB, Vol. 9:175, 2008.  
Keywords: distance between networks, phylogenetic network, phylogeny, Program Bio PhyloNetwork, tree sibling network, tree-child network.
Note: http://dx.doi.org/10.1186/1471-2105-9-175.
       
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Tobias Kloepper and Daniel H. Huson. Drawing explicit phylogenetic networks and their integration into SplitsTree. In BMCEB, Vol. 8(22), 2008.  
Keywords: explicit network, phylogenetic network, phylogeny, Program SplitsTree, software, split network, visualization.
Note: http://dx.doi.org/10.1186/1471-2148-8-22.
       
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Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi and Giancarlo Mauri. The Comparison of Phylogenetic Networks: Algorithms and Complexity. In Ion Mandoiu and Alexander Zelikovsky editors, Bioinformatics Algorithms, John Wiley and Sons Ltd, 2008.  
Keywords: phylogenetic network, phylogeny.
Note: http://www.amazon.com/gp/reader/0470097736/.
       

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Stefan Grünewald, Andreas Spillner, Kristoffer Forslund and Vincent Moulton. Constructing Phylogenetic Supernetworks from Quartets. In WABI08, Vol. 5251:284-295 of LNCS, springer, 2008.  
Keywords: abstract network, from quartets, from unrooted trees, phylogenetic network, phylogeny, Program QNet, Program SplitsTree, reconstruction, split network.
Note: http://dx.doi.org/10.1007/978-3-540-87361-7_24.
       
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Gabriel Cardona, Mercè Llabrés, Francesc Rosselló and Gabriel Valiente. Phylogenetic Networks: Justification, Models, Distances and Algorithms. In VI Jornadas de Matemática Discreta y Algorítmica (JMDA'08), 2008.  
Keywords: distance between networks, mu distance, phylogenetic network, phylogeny, polynomial, survey, time consistent network, tree-child network, tripartition distance, triplet distance.
Note: http://bioinfo.uib.es/media/uploaded/jmda2008_submission_61-1.pdf.
       

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Olivier Gauthier and François-Joseph Lapointe. Seeing the Trees for the Network: Consensus, Information Content, and Superphylogenies. In Systematic Biology, Vol. 56(2):345-355, 2007.  
Keywords: consensus.
Note: http://dx.doi.org/10.1080/10635150701286549.
       
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Barbara R. Holland, Glenn Conner, Katharina Huber and Vincent Moulton. Imputing Supertrees and Supernetworks from Quartets. In Systematic Biology, Vol. 56(1):57-67, 2007.  
Keywords: abstract network, from unrooted trees, phylogenetic network, phylogeny, Program Quartet, reconstruction, split network, supernetwork.
Note: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.99.3215.
       
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Daniel H. Huson. Split networks and Reticulate Networks. In Olivier Gascuel and Mike Steel editors, Reconstructing Evolution, New Mathematical and Computational Advances, Pages 247-276, Oxford University Press, 2007.  
Keywords: abstract network, consensus, from rooted trees, from sequences, from splits, from unrooted trees, galled tree, hybridization, phylogenetic network, phylogeny, Program Beagle, Program Spectronet, Program SplitsTree, Program SPNet, recombination, reconstruction, split network, survey.
Note: similar to http://www-ab.informatik.uni-tuebingen.de/research/phylonets/GCB2006.pdf.
       

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Daniel H. Huson and Tobias Kloepper. Beyond Galled Trees - Decomposition and Computation of Galled Networks. In RECOMB07, Vol. 4453:211-225 of LNCS, springer, 2007.  
Keywords: FPT, from splits, from trees, galled network, phylogenetic network, phylogeny, Program SplitsTree, reconstruction.
Note: http://dx.doi.org/10.1007/978-3-540-71681-5_15, errata..
       

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Cam Thach Nguyen, Nguyen Bao Nguyen and Wing-Kin Sung. Fast Algorithms for computing the Tripartition-based Distance between Phylogenetic Networks. In JCO, Vol. 13(3), 2007.  
Keywords: distance between networks, phylogenetic network, phylogeny, tripartition distance.
Note: http://dx.doi.org/10.1007/s10878-006-9025-5.
       
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Yufeng Wu and Dan Gusfield. Improved Algorithms for Inferring the Minimum Mosaic of a Set of Recombinants. In CPM07, Vol. 4580:150-161 of LNCS, springer, 2007.  
Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/CPM2007mosaic.pdf.
       

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Monique M. Morin. Phylogenetic Networks: Simulation, Characterization, and Reconstruction. PhD thesis, The University of New Mexico, U.S.A., 2007.  
Keywords: evaluation, explicit network, hybridization, lateral gene transfer, phylogenetic network, phylogeny, Program NetGen, simulation, software.
Note: http://www.cs.unm.edu/~morin/morin_phd.pdf.
       

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Bastienne Vriesendorp. Phylogenenetworks, exploring reticulate evolution and its consequences for phylogenetic reconstruction. PhD thesis, Wageningen University, The Netherlands, 2007.  
Keywords: consensus, distance between networks, evaluation, hybridization, median network, NeighborNet, parsimony, phylogenetic network, phylogeny, Program SplitsTree, split decomposition, survey.
Note: http://library.wur.nl/wda/dissertations/dis4239.pdf.
       

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Yuanyi Zhang. Optimization Algorithms for Phylogenetic Networks. PhD thesis, University of Texas at Dallas, U.S.A., 2007.  
Keywords: abstract network, explicit network, from distances, phylogenetic network, phylogeny, reconstruction, split, split network, visualization.
Note: http://proquest.umi.com/pqdlink?did=1421626541&sid=1&Fmt=6&clientId=176295&RQT=309&VName=PQD.
       

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Mihaela Baroni, Charles Semple and Mike Steel. Hybrids in Real Time. In Systematic Biology, Vol. 55(1):46-56, 2006.  
Keywords: agreement forest, from rooted trees, phylogenetic network, phylogeny, polynomial, reconstruction, time consistent network.
Note: http://www.math.canterbury.ac.nz/~m.steel/Non_UC/files/research/hybrids.pdf.
       
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Daniel H. Huson and David Bryant. Application of Phylogenetic Networks in Evolutionary Studies. In MBE, Vol. 23(2):254-267, 2006.  
Keywords: abstract network, phylogenetic network, phylogeny, Program SplitsTree, software, survey.
Note: http://dx.doi.org/10.1093/molbev/msj030, software available from www.splitstree.org.
       
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Jesper Jansson, Nguyen Bao Nguyen and Wing-Kin Sung. Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network. In SICOMP, Vol. 35(5):1098-1121, 2006. 1 comment  
Keywords: approximation, explicit network, from triplets, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.df.lth.se/~jj/Publications/triplets_to_gn7_SICOMP2006.pdf.
       
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Vladimir Makarenkov, Dmytro Kevorkov and Pierre Legendre. Phylogenetic Network Construction Approaches. In Applied Mycology and Biotechnology, Vol. 6:61-97, 2006.  
Keywords: from distances, hybridization, lateral gene transfer, median network, NeighborNet, netting, Program Arlequin, Program Network, Program Pyramids, Program Reticlad, Program SplitsTree, Program T REX, Program TCS, Program WeakHierarchies, pyramid, reticulogram, split, split decomposition, split network, survey, weak hierarchy.
Note: http://www.labunix.uqam.ca/~makarenv/makarenv/MKL_article.pdf.
       

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Monique M. Morin and Bernard M. E. Moret. NetGen: generating phylogenetic networks with diploid hybrids. In BIO, Vol. 22(15):1921-1923, 2006.  
Keywords: generation, hybridization, Program NetGen, software.
Note: http://dx.doi.org/10.1093/bioinformatics/btl191.
       
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Tetsuo Asano, Patricia Evans, Ryuhei Uehara and Gabriel Valiente. Site Consistency in Phylogenetic Networks with Recombination. In C. S. Iliopoulos, K. Park and K. Steinhöfel editors, Algorithms in Bioinformatics, Vol. 6:15-26 of Texts in Algorithmics, College Publications, 2006.  
       

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Guillaume Bourque and Louxin Zhang. Models and Methods in Comparative Genomics. In Chau-Wen Tseng editor, Advances in Computers, Special Volume: Computational Biology, Vol. 68, Elsevier, 2006.  
Keywords: from distances, from rooted trees, from sequences, galled tree, phylogenetic network, phylogeny, survey.
Note: http://www.math.nus.edu.sg/~matzlx/papers/CompGen_ZLX.pdf.
       

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Jesper Jansson, Nguyen Bao Nguyen and Wing-Kin Sung. Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network. In SODA05, Pages 349-358, 2005. 1 comment  
Keywords: approximation, explicit network, from triplets, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://portal.acm.org/citation.cfm?id=1070481.
       

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Cam Thach Nguyen, Nguyen Bao Nguyen and Wing-Kin Sung. Fast Algorithms for computing the Tripartition-based Distance between Phylogenetic Networks. In ISAAC05, Pages 402-411, 2005.  
Keywords: distance between networks, phylogenetic network, phylogeny, tripartition distance.
Note: http://www.cs.washington.edu/homes/ncthach/Papers/ISAAC2006.pdf.
       

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Richard C. Winkworth, David Bryant, Peter J. Lockhart, David Havell and Vincent Moulton. Biogeographic Interpretation of Splits Graphs: Least Squares Optimization of Branch Lengths. In Systematic Biology, Vol. 54(1):56-65, 2005.  
Keywords: abstract network, from distances, from network, phylogenetic network, phylogeny, reconstruction, split, split network.
Note: http://www.math.auckland.ac.nz/~bryant/Papers/05Biogeographic.pdf.
       

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David Bryant. Extending tree models to splits networks. In Lior Pachter and Bernd Sturmfels editors, Algebraic Statistics for Computational Biology, Pages 322-334, Cambridge University Press, 2005.  
Keywords: abstract network, from splits, likelihood, phylogenetic network, phylogeny, split, split network, statistical model.
Note: http://www.math.auckland.ac.nz/~bryant/Papers/05ascbChapter.pdf.
       

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Bastienne Vriesendorp and Freek T. Bakker. Reconstructing patterns of reticulate evolution in angiosperms: what can we do? In Taxon, Vol. 54(3):593-604, 2005.  
Note: results cited in http://library.wur.nl/wda/dissertations/dis4239.pdf.
       

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Wei-Shun Su, Tso-Ching Lee and Yaw-Ling Lin. Efficient Algorithms for Constructing Phylogenetic Networks with Restricted Recombinations. In NCS05, Pages 1-7, 2005.  
Keywords: explicit network, from sequences, phylogenetic network, phylogeny, reconstruction.
Note: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.168.6735.
       

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David Bryant and Vincent Moulton. NeighborNet: An Agglomerative Method for the Construction of Phylogenetic Networks. In MBE, Vol. 21(2):255-265, 2004.  
Keywords: phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network.
Note: http://www.math.auckland.ac.nz/~bryant/Papers/04NeighborNet.pdf.
       
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Andreas W. M. Dress and Daniel H. Huson. Constructing splits graphs. In TCBB, Vol. 1(3):109-115, 2004.  
Keywords: abstract network, circular split system, from trees, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network, visualization.
Note: http://scilib.kiev.ua/ieee/tcbb/2004/03/n3/n0109.pdf.
       
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105
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Daniel H. Huson, Tobias Dezulian, Tobias Kloepper and Mike Steel. Phylogenetic Super-Networks from Partial Trees. In TCBB, Vol. 1(4):151-158, 2004.  
Keywords: abstract network, from unrooted trees, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, supernetwork.
Note: http://hdl.handle.net/10092/3177.
       
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Mike Hallett and Jens Lagergren. Efficient algorithms for lateral gene transfers problems. 2004.  
Keywords: from rooted trees, lateral gene transfer, NP complete, phylogeny, polynomial, reconstruction.
Note: submitted to SIAM Journal on Computing, http://www.mcb.mcgill.ca/~hallett/Lateral.pdf.
       

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C. Randal Linder, Bernard M. E. Moret, Luay Nakhleh and Tandy Warnow. Network (Reticulate) Evolution: Biology, Models, and Algorithms. In PSB04, 2004.  
Note: http://www.cs.rice.edu/~nakhleh/Papers/psb04.pdf.
       

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Daniel H. Huson. What If I Don't Have a Tree? Split Decomposition and Related Models. In Current Protocols in Bioinformatics, Vol. Unit 6.7, 2003.  
Keywords: abstract network, phylogenetic network, Program SplitsTree, software, split decomposition, split network.
Note: http://dx.doi.org/10.1002/0471250953.bi0607s01.
       

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David Bryant and Vincent Moulton. Neighbor-Net: An Agglomerative Method for the Construction of Planar Phylogenetic Networks. In WABI02, Vol. 2452:375-391 of LNCS, springer, 2002.  
Keywords: abstract network, circular split system, from distances, NeighborNet, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network.
Note: http://dx.doi.org/10.1007/3-540-45784-4_28.
       

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Mike Hallett and Jens Lagergren. Efficient algorithms for lateral gene transfers problems. In RECOMB01, Pages 141-148, 2001.  
Keywords: from rooted trees, lateral gene transfer, NP complete, phylogeny, polynomial, Program McKiTscH, reconstruction.
Note: http://dx.doi.org/10.1145/369133.369188.
       

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David Posada and Keith A. Crandall. Intraspecific gene genealogies: trees grafting into networks. In TEE, Vol. 16(1):37-45, 2001.  
Keywords: likelihood, median network, netting, parsimony, phylogenetic network, phylogeny, Program Arlequin, Program SplitsTree, Program T REX, Program TCS, pyramid, reticulogram, split decomposition, statistical parsimony, survey.
Note: http://darwin.uvigo.es/download/papers/09.networks01.pdf.
       

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François-Joseph Lapointe. How to account for reticulation events in phylogenetic analysis: A review of distance-based methods. In Journal of Classification, Vol. 17:175-184, 2000.  
Keywords: abstract network, evaluation, from distances, phylogenetic network, Program Pyramids, Program SplitsTree, Program T REX, pyramid, reconstruction, reticulogram, split network, survey, weak hierarchy.
Note: http://dx.doi.org/10.1007/s003570000016.
       

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Mikkel H. Schierup and Jotun Hein. Recombination and the molecular clock. In MBE, Vol. 17(10):1578-1579, 2000.  
Note: http://www.birc.dk/Publications/Articles/Schierup_2000c.pdf.
       

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Vincent Berry and David Bryant. Faster reliable phylogenetic analysis. In RECOMB99, Pages 59-68, 1999.  
Keywords: abstract network, from quartets, phylogenetic network, phylogeny, polynomial, Program SplitsTree, reconstruction, split network, weakly compatible.
Note: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.95.9151.
       

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Daniel H. Huson. SplitsTree: analyzing and visualizing evolutionary data. In BIO, Vol. 14(1):68-73, 1998.  
Keywords: abstract network, phylogenetic network, phylogeny, Program SplitsTree, software, split network.
Note: http://bioweb.pasteur.fr/docs/doc-gensoft/splitstree/splitstree.ps.
       

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Andreas W. M. Dress, Daniel H. Huson and Vincent Moulton. Analyzing and visualizing distance data using SplitsTree. In DAM, Vol. 71(1):95-109, 1996.  
Keywords: abstract network, from distances, phylogenetic network, phylogeny, Program SplitsTree, software, split network, visualization.
Note: http://bibiserv.techfak.uni-bielefeld.de/splits/splits.pdf.
       

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Daniel H. Huson and Rainer Wetzel. Analyzing and visualizing sequence and distance data with SplitsTree V1.0.2. 1995.  
Keywords: abstract network, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, software, split network, visualization.
Note: Technical report, http://citeseer.ist.psu.edu/173442.html.
       

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Laurent Excoffier and Peter E. Smouse. Using Allele Frequencies and Geographic Subdivision to Reconstruct Gene Trees Within a Species: Molecular Variance Parsimony. In GEN, Vol. 136:343-359, 1994.  
Keywords: from distances, minimum spanning network, phylogenetic network, phylogeny, Program Arlequin, reconstruction, software.
Note: http://www.genetics.org/cgi/content/abstract/136/1/343.
       

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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.
       

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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.
       

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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.
       

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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.
       

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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.
       

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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.
       

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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.
       

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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.
       

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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.
       

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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.
       

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

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

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

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

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

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

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

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

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

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

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

140
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Katharina Huber, Leo van Iersel, Remie Janssen, Mark Jones, Vincent Moulton, Yukihiro Murakami and Charles Semple. Rooting for phylogenetic networks. 2019.  
Keywords: explicit network, from network, level k phylogenetic network, orchard network, orientation, phylogenetic network, phylogeny, reconstruction, stack-free network, tree-based network, tree-child network, valid network.
Note: https://arxiv.org/abs/1906.07430.
       

141
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Daniel H. Huson and Simone Linz. Autumn Algorithm - Computation of Hybridization Networks for Realistic Phylogenetic Trees. In TCBB, Vol. 15:398-410, 2018.  
Keywords: explicit network, from rooted trees, phylogenetic network, phylogeny, Program Dendroscope, reconstruction.
Note: https://simonelinz.files.wordpress.com/2016/06/hl16.pdf.
       

142
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Mathias Weller. Linear-Time Tree Containment in Phylogenetic Networks. In RECOMB-CG18, Vol. 11183:309-323 of LNCS, Springer, 2018.  
Keywords: explicit network, from network, from rooted trees, nearly-stable network, phylogenetic network, phylogeny, polynomial, reconstruction, reticulation-visible network, tree containment.
Note: https://arxiv.org/abs/1702.06364.
       

143
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Andrew R. Francis, Katharina Huber, Vincent Moulton and Taoyang Wu. Bounds for phylogenetic network space metrics. In JOMB, Vol. 76(5):1229-1248, 2018.  
Keywords: bound, distance between networks, from network, NNI distance, NNI moves, phylogenetic network, phylogeny, SPR distance, TBR distance.
Note: https://arxiv.org/abs/1702.05609.
       

144
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Andreas Gunawan. Solving the Tree Containment Problem for Reticulation-visible Networks in Linear Time. In AlCoB18, Vol. 10849:24-36 of LNCS, Springer, 2018.  
Keywords: explicit network, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulation-visible network, tree containment.
Note: https://arxiv.org/abs/1702.04088.
       

145
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Philippe Gambette, Andreas Gunawan, Anthony Labarre, Stéphane Vialette and Louxin Zhang. Solving the Tree Containment Problem in Linear Time for Nearly Stable Phylogenetic Networks. In DAM, Vol. 246:62-79, 2018.  
Keywords: explicit network, from network, from rooted trees, nearly-stable network, phylogenetic network, phylogeny, polynomial, tree containment.
Note: https://hal-upec-upem.archives-ouvertes.fr/hal-01575001/en/.
       

146
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Remie Janssen, Mark Jones, Péter L. Erdös, Leo van Iersel and Celine Scornavacca. Exploring the tiers of rooted phylogenetic network space using tail moves. In BMB, Vol. 80(8):2177-2208, 2018.  
Keywords: distance between networks, explicit network, from network, NNI moves, orientation, phylogenetic network, phylogeny, SPR distance.
Note: https://arxiv.org/abs/1708.07656.
       

147
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Sebastien Roch and Kun-Chieh Wang. Circular Networks from Distorted Metrics. In RECOMB18, Vol. 10812:167-176 of LNCS, Springer, 2018.  
Keywords: abstract network, circular split system, from distances, NeighborNet, phylogenetic network, phylogeny, reconstruction, split network.
Note: https://arxiv.org/abs/1707.05722.
       

148
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Paul Bastide, Claudia Solís-Lemus, Ricardo Kriebel, Kenneth William Sparks and Cécile Ané. Phylogenetic Comparative Methods on Phylogenetic Networks with Reticulations. In SB, Vol. 67(5):800-820, 2018.  
Keywords: ancestral trait reconstruction, from network, likelihood, Program PhyloNetworks SNaQ, software, statistical model, statistical test.
Note: https://doi.org/10.1101/194050.
       

149
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Katharina Huber, Vincent Moulton, Charles Semple and Taoyang Wu. Quarnet inference rules for level-1 networks. In BMB, Vol. 80:2137-2153, 2018.  
Keywords: explicit network, from quarnets, from subnetworks, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction.
Note: https://arxiv.org/abs/1711.06720.
       

150
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Leo van Iersel, Mark Jones and Celine Scornavacca. Improved maximum parsimony models for phylogenetic networks. In SB, Vol. 67(3):518-542, 2018.  
Keywords: explicit network, FPT, from sequences, NP complete, parsimony, phylogenetic network, phylogeny, reconstruction, weakly displaying.
Note: https://leovaniersel.files.wordpress.com/2017/12/improved_parsimony_networks.pdf.
       

151
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Magnus Bordewich, Katharina Huber, Vincent Moulton and Charles Semple. Recovering normal networks from shortest inter-taxa distance information. In JOMB, Vol. 77(3):571-594, 2018.  
Keywords: explicit network, from distances, normal network, phylogenetic network, phylogeny, polynomial, reconstruction, uniqueness.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BHMS18.pdf.
       

152
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Kuang-Yu Chang, Yun Cui, Siu-Ming Yiu and Wing-Kai Hon. Reconstructing One-Articulated Networks with Distance Matrices. In JCB, Vol. 25(3):253-269, 2018.  
Keywords: explicit network, from distances, k-reticulated, phylogenetic network, phylogeny, reconstruction.
       

153
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Kuang-Yu Chang, Wing-Kai Hon and Sharma V. Thankachan. Compact Encoding for Galled-Trees and its Applications. In 2018 Data Compression Conference, Pages 297-306, 2018.  
Keywords: compression, counting, explicit network, galled tree, phylogenetic network, polynomial.
       

154
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Hongwei Yan, Andreas Gunawan and Louxin Zhang. S-Cluster++: a fast program for solving the cluster containment problem for phylogenetic networks. In BIO, Vol. 34(17):i680–i686, 2018.  
Keywords: cluster containment, explicit network, phylogenetic network, phylogeny, SAT.
Note: http://dx.doi.org/10.1093/bioinformatics/bty594.
       

155
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Dingqiao Wen, Yun Yu, Jiafan Zhu and Luay Nakhleh. Inferring Phylogenetic Networks Using PhyloNet. In SB, Vol. 67(4):735-740, 2018.  
Keywords: bayesian, likelihood, parsimony, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, software.
       

156
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Dingqiao Wen and Luay Nakhleh. Coestimating Reticulate Phylogenies and Gene Trees from Multilocus Sequence Data. In SB, Vol. 67(3):439-457, 2018.  
Keywords: bayesian, explicit network, from sequences, incomplete lineage sorting, phylogenetic network, phylogeny, Program PhyloNet, reconstruction.
Note: https://doi.org/10.1093/sysbio/syx085.
       

157
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Andreas Gunawan. On the tree and cluster containment problems for phylogenetic networks. PhD thesis, National University of Singapore, 2018.  
Keywords: cluster containment, explicit network, galled network, genetically stable network, nearly-stable network, phylogenetic network, phylogeny, reticulation-visible network, tree containment.
Note: https://scholarbank.nus.edu.sg/handle/10635/144270.
       

158
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Katharina Huber, Leo van Iersel, Vincent Moulton, Celine Scornavacca and Taoyang Wu. Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets. In ALG, Vol. 77(1):173-200, 2017.  
Keywords: explicit network, FPT, from binets, from subnetworks, from trinets, NP complete, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://arxiv.org/abs/1411.6804.
       

159
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Monika Balvociute, David Bryant and Andreas Spillner. When can splits be drawn in the plane? In SIAM Journal on Discrete Mathematics, Vol. 31(2):839-856, 2017.  
Keywords: abstract network, characterization, flat, phylogenetic network, planar, split, split network.
Note: http://arxiv.org/abs/1509.06104v1.
       

160
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Satyan L. Devadoss and Samantha Petti. A Space of Phylogenetic Networks. In SIAM Journal on Applied Algebra and Geometry, Vol. 1(1):683-705, 2017.  
Keywords: abstract network, circular split system, phylogenetic network, phylogeny, split network.
Note: http://arxiv.org/abs/1607.06978.
       

161
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Philippe Gambette, Katharina Huber and Guillaume Scholz. Uprooted Phylogenetic Networks. In BMB, Vol. 79(9):2022-2048, 2017.  
Keywords: circular split system, explicit network, from splits, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction, split network, uniqueness.
Note: http://arxiv.org/abs/1511.08387.
       

162
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Julia Matsieva, Steven Kelk, Celine Scornavacca, Chris Whidden and Dan Gusfield. A Resolution of the Static Formulation Question for the Problem of Computing the History Bound. In TCBB, Vol. 14(2):404-417, 2017.  
Keywords: ARG, explicit network, from sequences, minimum number, phylogenetic network, phylogeny.
       

163
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Sha Zhu and James H. Degnan. Displayed Trees Do Not Determine Distinguishability Under the Network Multispecies Coalescent. In SB, Vol. 66(2):283-298, 2017.  
Keywords: branch length, coalescent, explicit network, from network, likelihood, phylogenetic network, phylogeny, Program Hybrid-coal, Program Hybrid-Lambda, Program PhyloNet, software, uniqueness.
Note: presentation available at https://www.youtube.com/watch?v=JLYGTfEZG7g.
       

164
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Vincent Moulton, James Oldman and Taoyang Wu. A cubic-time algorithm for computing the trinet distance between level-1 networks. In IPL, Vol. 123:36-41, 2017.  
Keywords: distance between networks, explicit network, from network, phylogenetic network, phylogeny, polynomial, Program TriLoNet.
Note: https://doi.org/10.1016/j.ipl.2017.03.002.
       

165
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Olga K. Kamneva and Noah A. Rosenberg. Simulation-Based Evaluation of Hybridization Network Reconstruction Methods in the Presence of Incomplete Lineage Sorting. In Evolutionary Bioinformatics, Vol. 13(1176934317691935):1-16, 2017.  
Keywords: evaluation, explicit network, incomplete lineage sorting, simulation.
Note: https://dx.doi.org/10.1177%2F1176934317691935.
       

166
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Celine Scornavacca, Joan Carles Pons and Gabriel Cardona. Fast algorithm for the reconciliation of gene trees and LGT networks. In JTB, Vol. 418:129-137, 2017.  
Keywords: duplication, explicit network, from network, from rooted trees, lateral gene transfer, LGT network, loss, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction.
       

167
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Jesper Jansson, Ramesh Rajaby and Wing-Kin Sung. An Efficient Algorithm for the Rooted Triplet Distance Between Galled Trees. In AlCoB17, Vol. 10252:115-126 of LNCS, Springer, 2017.  
Keywords: distance between networks, from network, phylogenetic network, phylogeny, polynomial, reconstruction, triplet distance.
Note: .
       

168
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Leo van Iersel, Vincent Moulton, Eveline De Swart and Taoyang Wu. Binets: fundamental building blocks for phylogenetic networks. In BMB, Vol. 79(5):1135-1154, 2017.  
Keywords: approximation, explicit network, from binets, from subnetworks, galled tree, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1007/s11538-017-0275-4.
       

169
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Han Lai, Maureen Stolzer and Dannie Durand. Fast Heuristics for Resolving Weakly Supported Branches Using Duplication, Transfers, and Losses. In RECOMB-CG17, Vol. 10562:298-320 of LNCS, Springer, 2017.  
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program Notung, reconstruction.
       

170
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Claudia Solís-Lemus, Paul Bastide and Cécile Ané. PhyloNetworks: A Package for Phylogenetic Networks. In MBE, Vol. 34(12):3292-3298, 2017.  
Keywords: from sequences, from trees, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, reconstruction, software.
Note: https://doi.org/10.1093/molbev/msx235.
       

171
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Ruzbeh Tusserkani, Hadi Poormohammadi, Azin Azadi and Changiz Eslahchi. Inferring phylogenies from minimal information. In AEEICB17, Pages 202-206, IEEE, 2017.  
Keywords: from triplets, phylogenetic network, phylogeny, Program TripNet, reconstruction.
       

172
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Klaus Schliep, Alastair J. Potts, David A. Morrison and Guido W. Grimm. Intertwining phylogenetic trees and networks. In Methods in Ecology and Evolution, Vol. 8(10):1212-1220, 2017.  
Keywords: abstract network, from network, from unrooted trees, phylogenetic network, phylogeny, split network, visualization.
Note: http://dx.doi.org/10.1111/2041-210X.12760.
       

173

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

174
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Mohammad Hossein Reyhani and Hadi Poormohammadi. RPNCH: A Method for Constructing Rooted Phylogenetic Networks from Rooted Triplets based on Height Function. In Archives of Advances in Biosciences, Vol. 8(4):14-20, 2017.  
Keywords: explicit network, from triplets, heuristic, phylogenetic network, phylogeny, reconstruction.
Note: http://journals.sbmu.ac.ir/jps/article/view/16707.
       

175
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Edwin Jacox, Mathias Weller, Eric Tannier and Celine Scornavacca. Resolution and reconciliation of non-binary gene trees with transfers, duplications and losses. In BIO, Vol. 33(7):980-987, 2017.  
Keywords: duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1093/bioinformatics/btw778.
       

176
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Luay Nakhleh. Phylogenetic Networks: From Displayed Trees to a Distribution of Gene Trees. Phyloseminar #70, 2017.  
Keywords: bayesian, coalescent, explicit network, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, statistical model.
Note: https://www.youtube.com/watch?v=dkQsvLUUDcQ.
       

177
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Celine Scornavacca. Occam's razor in phylogenetic network reconstruction. Phyloseminar #71, 2017.  
Keywords: explicit network, from rooted trees, parsimony, phylogenetic network, phylogeny, reconstruction.
Note: https://www.youtube.com/watch?v=W6tEVulgQu8.
       

178
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Cécile Ané. From reconstructing to using phylogenetic networks. Phyloseminar #72, 2017.  
Keywords: explicit network, from sequences, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, reconstruction, semidirected network.
Note: https://www.youtube.com/watch?v=PF4j_JOQP0c.
       

179
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Paul Bastide. Shifted stochastic processes evolving on trees : application to models of adaptive evolution on phylogenies. PhD thesis, Université Paris Saclay, 2017.  
Keywords: ancestral trait reconstruction, bayesian, explicit network, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, reconstruction, statistical model.
Note: https://tel.archives-ouvertes.fr/tel-01629648/en/, slides..
       

180
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Kuang-Yu Chang, Yun Cui, Siu-Ming Yiu and Wing-Kai Hon. Reconstructing One-Articulated Networks with Distance Matrices. In ISBRA17, Vol. 10330:34-45 of LNCS, Springer, 2017.  
Keywords: explicit network, from distances, k-reticulated, phylogenetic network, phylogeny, reconstruction.
Note: https://link.springer.com/content/pdf/10.1007%2F978-3-319-59575-7.pdf#page=100.
       

181
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Leo van Iersel, Steven Kelk, Nela Lekic, Chris Whidden and Norbert Zeh. Hybridization Number on Three Rooted Binary Trees is EPT. In SIDMA, Vol. 30(3):1607-1631, 2016.  
Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1402.2136.
       

182
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Steven Kelk, Leo van Iersel, Celine Scornavacca and Mathias Weller. Phylogenetic incongruence through the lens of Monadic Second Order logic. In JGAA, Vol. 20(2):189-215, 2016.  
Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, MSOL, phylogenetic network, phylogeny, reconstruction.
Note: http://jgaa.info/accepted/2016/KelkIerselScornavaccaWeller2016.20.2.pdf.
       

183
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Sajad Mirzaei and Yufeng Wu. Fast Construction of Near Parsimonious Hybridization Networks for Multiple Phylogenetic Trees. In TCBB, Vol. 13(3):565-570, 2016.  
Keywords: bound, explicit network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program PIRN, reconstruction, software.
Note: http://www.engr.uconn.edu/~ywu/Papers/PIRNs-preprint.pdf.
       

184
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Philippe Gambette, Andreas Gunawan, Anthony Labarre, Stéphane Vialette and Louxin Zhang. Solving the Tree Containment Problem for Genetically Stable Networks in Quadratic Time. In IWOCA15, Vol. 9538:197-208 of LNCS, springer, 2016.  
Keywords: explicit network, from network, from rooted trees, genetically stable network, phylogenetic network, phylogeny, polynomial, tree containment.
Note: https://hal-upec-upem.archives-ouvertes.fr/hal-01226035 .
       

185
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Vincent Ranwez, Celine Scornavacca, Jean-Philippe Doyon and Vincent Berry. Inferring gene duplications, transfers and losses can be done in a discrete framework. In JOMB, Vol. 72(7):1811-1844, 2016.  
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction.
       

186
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Claudia Solís-Lemus and Cécile Ané. Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting. In PLOS Genetics, Vol. 12(3):e1005896, 2016.  
Keywords: explicit network, from quartets, from unrooted trees, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ.
Note: http://arxiv.org/abs/1509.06075v1.
       

187
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François Chevenet, Jean-Philippe Doyon, Celine Scornavacca, Edwin Jacox, Emmanuelle Jousselin and Vincent Berry. SylvX: a viewer for phylogenetic tree reconciliations. In BIO, Vol. 32(4):608-610, 2016.  
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program SylvX, software, visualization.
Note: https://www.researchgate.net/profile/Emmanuelle_Jousselin/publication/283446016_SylvX_a_viewer_for_phylogenetic_tree_reconciliations/links/5642146108aec448fa621efa.pdf.
       

188
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Rinku Mathur and Neeru Adlakha. A graph theoretic model for prediction of reticulation events and phylogenetic networks for DNA sequences. In Egyptian Journal of Basic and Applied Sciences, Vol. 3(3):263-271, 2016.  
Keywords: from sequences, phylogenetic network, phylogeny, Program T REX.
Note: http://dx.doi.org/10.1016/j.ejbas.2016.07.004.
       

189
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Andreas Gunawan, Bingxin Lu and Louxin Zhang. A program for verification of phylogenetic network models. In ECCB16, Vol. 32(17):i503-i510 of BIO, 2016.  
Keywords: exponential algorithm, from network, from rooted trees, phylogenetic network, phylogeny, software, tree containment.
Note: http://dx.doi.org/10.1093/bioinformatics/btw467.
       

190
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Hussein A. Hejase and Kevin J. Liu. A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation. Vol. 17(422):1-12, 2016.  
Keywords: abstract network, evaluation, from sequences, phylogenetic network, phylogeny, Program PhyloNet, Program PhyloNetworks SNaQ, reconstruction, simulation, unicyclic network.
Note: http://dx.doi.org/10.1186/s12859-016-1277-1.
       

191
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Benjamin Albrecht. Computing Hybridization Networks Using Agreement Forests. PhD thesis, Ludwig-Maximilians-Universität München, 2016.  
Note: https://edoc.ub.uni-muenchen.de/19444/.
       

192
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Philippe Gambette, Leo van Iersel, Steven Kelk, Fabio Pardi and Celine Scornavacca. Do branch lengths help to locate a tree in a phylogenetic network? In BMB, Vol. 78(9):1773-1795, 2016.  
Keywords: branch length, explicit network, FPT, from network, from rooted trees, NP complete, phylogenetic network, phylogeny, pseudo-polynomial, time consistent network, tree containment, tree sibling network.
Note: http://arxiv.org/abs/1607.06285.
       

193
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Katharina Huber, Vincent Moulton and Taoyang Wu. Transforming phylogenetic networks: Moving beyond tree space. In JTB, Vol. 404:30-39, 2016.  
Keywords: distance between networks, level k phylogenetic network, NNI moves, phylogenetic network, phylogeny.
Note: http://arxiv.org/abs/1601.01788.
       

194
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James Oldman, Taoyang Wu, Leo van Iersel and Vincent Moulton. TriLoNet: Piecing together small networks to reconstruct reticulate evolutionary histories. In MBE, Vol. 33(8):2151-2162, 2016.  
Keywords: explicit network, from subnetworks, from trinets, galled tree, phylogenetic network, phylogeny, Program LEV1ATHAN, Program TriLoNet, reconstruction.
       

195
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Dingqiao Wen, Yun Yu and Luay Nakhleh. Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent. In PLoS Genetics, Vol. 12(5):e1006006, 2016.  
Keywords: bayesian, coalescent, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, software.
       

196
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Magnus Bordewich and Nihan Tokac. An algorithm for reconstructing ultrametric tree-child networks from inter-taxa distances. In DAM, Vol. 213:47-59, 2016.  
Keywords: explicit network, from distances, phylogenetic network, phylogeny, reconstruction, tree-child network.
Note: http://dx.doi.org/10.1016/j.dam.2016.05.011.
       

197
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Dan Graur. Reticulate evolution and phylogenetic networks. In Molecular and Genome Evolution, Chapter 6, Sinauer, 2016.  
Keywords: phylogenetic network, phylogeny, survey.
Note: http://www.sinauer.com/media/wysiwyg/samples/Graur_MGE1e_Ch06.pdf.
       

198
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Juan Wang. A Survey of Methods for Constructing Rooted Phylogenetic Networks. In PLoS ONE, Vol. 11(11):e0165834, 2016.  
Keywords: evaluation, explicit network, from clusters, phylogenetic network, phylogeny, Program BIMLR, Program Dendroscope, Program LNetwork, reconstruction, survey.
Note: http://dx.doi.org/10.1371/journal.pone.0165834.
       

199
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Nihan Tokac. Efficiency of Algorithms in Phylogenetics. PhD thesis, Durham University, U.K., 2016.  
Keywords: explicit network, from distances, phylogenetic network, phylogeny, reconstruction, tree-child network.
Note: http://etheses.dur.ac.uk/11768/.
       

200
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Leo van Iersel, Steven Kelk and Celine Scornavacca. Kernelizations for the hybridization number problem on multiple nonbinary trees. In JCSS, Vol. 82(6):1075-1089, 2016.  
Keywords: explicit network, from rooted trees, kernelization, minimum number, phylogenetic network, phylogeny, Program Treeduce, reconstruction.
Note: https://arxiv.org/abs/1311.4045v3.
       

201
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Edwin Jacox, Cédric Chauve, Gergely J. Szöllösi, Yann Ponty and Celine Scornavacca. EcceTERA: comprehensive gene tree-species tree reconciliation using parsimony. In BIO, Vol. 32(13):2056-2058, 2016.  
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, parsimony, phylogenetic network, phylogeny, polynomial, Program ecceTERA.
Note: https://doi.org/10.1093/bioinformatics/btw105.
       

202
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Pei Wu. Quartet weights in phylogenetic network reconstruction. PhD thesis, University of Chinese Academy of Sciences, 2016.  
Keywords: abstract network, from distances, from quartets, phylogenetic network, phylogeny, reconstruction, split, split network.
Note: https://www.researchgate.net/publication/324475948_Quartet_weights_in_phylogenetic_network_reconstruction.
       

203
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Dingqiao Wen. Bayesian Inference of Phylogenetic Networks. Master's thesis, Rice University, Texas, 2016.  
Keywords: bayesian, explicit network, phylogenetic network, phylogeny, Program PhyloNet, reconstruction.
Note: https://scholarship.rice.edu/bitstream/handle/1911/96515/WEN-DOCUMENT-2016.pdf?sequence=1&isAllowed=y.
       

204
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Mareike Fischer, Leo van Iersel, Steven Kelk and Celine Scornavacca. On Computing The Maximum Parsimony Score Of A Phylogenetic Network. In SIDMA, Vol. 29(1):559-585, 2015.  
Keywords: APX hard, cluster containment, explicit network, FPT, from network, from sequences, integer linear programming, level k phylogenetic network, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, Program MPNet, reconstruction, software.
Note: http://arxiv.org/abs/1302.2430.
       

205
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Andrew R. Francis and Mike Steel. Which phylogenetic networks are merely trees with additional arcs? In Systematic Biology, Vol. 64(5):768-777, 2015.  
Keywords: explicit network, phylogenetic network, phylogeny, polynomial, tree-based network.
Note: http://arxiv.org/abs/1502.07045.
       

206
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Philippe Gambette, Andreas Gunawan, Anthony Labarre, Stéphane Vialette and Louxin Zhang. Locating a Tree in A Phylogenetic Network in Quadratic Time. In RECOMB15, Vol. 9029:96-107 of LNCS, Springer, 2015.  
Keywords: evaluation, explicit network, from network, from rooted trees, genetically stable network, nearly-stable network, phylogenetic network, phylogeny, polynomial, tree containment.
Note: https://hal.archives-ouvertes.fr/hal-01116231/en.
       

207
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Quan Nguyen. Likelihood-based Phylogenetic Network Inference by Approximate Structural Expectation Maximization. Master's thesis, University of Helsinki, 2015.  
Keywords: BIC, likelihood, phylogenetic network, phylogeny, Program PhyloDAG, reconstruction, software.
Note: http://urn.fi/URN:NBN:fi-fe2015062910525.
       

208
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Quan Nguyen and Teemu Roos. Likelihood-based inference of phylogenetic networks from sequence data by PhyloDAG. In AlCoB15, Vol. 9199:126-140 of LNCS, springer, 2015.  
Keywords: BIC, explicit network, from sequences, likelihood, phylogenetic network, phylogeny, Program PhyloDAG, reconstruction, software.
Note: http://www.cs.helsinki.fi/u/ttonteri/pub/alcob2015.pdf.
       

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

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

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

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

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

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

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

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

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

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Marc Thuillard and Didier Fraix-Burnet. Phylogenetic Trees and Networks Reduce to Phylogenies on Binary States: Does It Furnish an Explanation to the Robustness of Phylogenetic Trees against Lateral Transfers? In Evolutionary Bioin