Publications related to 'software' : Publications tagged by 'software' describe a software usually available from the internet. A list of all software dedicated to phylogenetic networks is available here.
 
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Associated keywords
abstract-network agreement-forest approximation APX-hard ARG bayesian BIC bound branch-and-bound branch-length circular-split-system cluster-containment coalescent consistency duplication evaluation explicit-network exponential-algorithm FPT from-clusters from-distances from-multilabeled-tree from-network from-quartets from-rooted-trees from-sequences from-species-tree from-splits from-trees from-triplets from-unrooted-trees galled-tree generation haplotype-network heuristic hybridization incomplete-lineage-sorting integer-linear-programming lateral-gene-transfer level-k-phylogenetic-network likelihood lineage-sorting loss median-network MedianJoining minimum-number minimum-spanning-network NeighborNet NP-complete parsimony phylogenetic-network phylogeny polynomial population-genetics Program-Arlequin Program-Beagle Program-BIMLR Program-Clustistic Program-CMPT Program-CombineTrees Program-CycleKiller Program-Dendroscope Program-EEEP Program-FastHN Program-FlatNJ Program-Fylogenetica Program-GalledTree Program-HGT_simul Program-HorizStory Program-Hybrid-coal Program-Hybrid-Lambda Program-HybridInterleave Program-HybridNET Program-Hybroscale Program-LatTrans Program-LEV1ATHAN Program-Lev1Generator Program-LGTnetwork Program-LNetwork Program-MaafB Program-MC-Net Program-Mowgli Program-MowgliNNI Program-MPNet Program-NetGen Program-NetTest Program-Network Program-PADRE Program-Phangorn Program-PhippsNetwork Program-PhyloDAG Program-PhyloNet Program-PhyloNetworks-SNaQ Program-PIRN Program-PopART Program-Prunier Program-Pyramids Program-QNet Program-Quartet-Decomposition Program-Recodon Program-RecPars Program-SAQ-Net Program-Serial-NetEvolve Program-Sliding-MinPD Program-SNSA Program-Spectronet Program-SplitsTree Program-SPNet Program-SuperQ Program-SylvX Program-T-REX Program-TCS Program-Treevolve Program-TripNet pyramid recombination recombination-detection reconstruction reticulogram serial-evolutionary-networks simulated-annealing simulation software split split-decomposition split-network SPR-distance statistical-model statistical-parsimony survey time-consistent-network tree-child-network tree-containment tree-sibling-network tree-based-network uniqueness visualization
Article (Journal)
1
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Jean-Christophe Aude, Yolande Diaz-Lazcoz, Jean-Jacques Codani and Jean-Loup Risler. Applications of the Pyramidal Clustering Method to Biological Objects. In CC, Vol. 23(3-4):303-315, 1999.  
Keywords: from distances, phylogenetic network, phylogeny, Program Pyramids, pyramid, reconstruction, software, visualization.
Note: http://dx.doi.org/10.1016/S0097-8485(99)00006-6.
       

2
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Hans-Jürgen Bandelt, Peter Forster and Arne Röhl. Median-joining networks for inferring intraspecies phylogenies. In MBE, Vol. 16(1):37-48, 1999.  
Keywords: from sequences, median network, MedianJoining, Program Network, reconstruction, software.
Note: http://mbe.oxfordjournals.org/cgi/content/abstract/16/1/37.
       

3
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Mark Clement, David Posada and Keith A. Crandall. TCS: a computer program to estimate gene genealogies. In MOLE, Vol. 9:1657-1659, 2000.  
Keywords: from sequences, parsimony, phylogenetic network, phylogeny, Program TCS, reconstruction, software, statistical parsimony.
Note: http://darwin.uvigo.es/download/papers/08.tcs00.pdf.
       
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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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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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Stefan Grünewald, Kristoffer Forslund, Andreas W. M. Dress and Vincent Moulton. QNet: An agglomerative method for the construction of phylogenetic networks from weighted quartets. In MBE, Vol. 24(2):532-538, 2007.  
Keywords: abstract network, circular split system, from quartets, phylogenetic network, phylogeny, Program QNet, reconstruction, software.
Note: http://mbe.oxfordjournals.org/cgi/content/abstract/24/2/532.
       
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Stefan Grünewald, Vincent Moulton and Andreas Spillner. Consistency of the QNet algorithm for generating planar split networks from weighted quartets. In DAM, Vol. 157(10):2325-2334, 2009.  
Keywords: abstract network, consistency, from quartets, phylogenetic network, phylogeny, Program QNet, reconstruction, software.
Note: http://dx.doi.org/10.1016/j.dam.2008.06.038.
       
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Jotun Hein. A heuristic method to reconstruct the history of sequences subject to recombination. In JME, Vol. 36(4):396-405, 1993.  
Keywords: explicit network, from sequences, heuristic, parsimony, phylogenetic network, phylogeny, Program RecPars, recombination, recombination detection, software.
Note: http://dx.doi.org/10.1007/BF00182187.
       

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Katharina Huber, Michael Langton, David Penny, Vincent Moulton and Mike Hendy. Spectronet: A package for computing spectra and median networks. In ABIO, Vol. 1(3):159-161, 2004.  
Keywords: from splits, median network, phylogenetic network, phylogeny, Program Spectronet, software, split, visualization.
Note: http://citeseer.ist.psu.edu/631776.html.
       
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Katharina Huber, Bengt Oxelman, Martin Lott and Vincent Moulton. Reconstructing the Evolutionary History of Polyploids from Multilabeled Trees. In MBE, Vol. 23(9):1784-1791, 2007.  
Keywords: duplication, explicit network, from multilabeled tree, from trees, phylogenetic network, phylogeny, Program PADRE, reconstruction, software.
Note: http://mbe.oxfordjournals.org/cgi/content/full/23/9/1784.
       
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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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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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Vladimir Makarenkov. T-REX: reconstructing and visualizing phylogenetic trees and reticulation networks. In BIO, Vol. 17(7):664-668, 2001.  
Keywords: phylogenetic network, phylogeny, Program T REX, reconstruction, reticulogram, software, visualization.
Note: http://www.labunix.uqam.ca/~makarenv/makarenv/Article_BIO.pdf.
       

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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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Luay Nakhleh, Tandy Warnow, C. Randal Linder and Katherine St. John. Reconstructing reticulate evolution in species - theory and practice. In JCB, Vol. 12(6):796-811, 2005.  
Keywords: from rooted trees, galled tree, phylogenetic network, phylogeny, polynomial, Program SPNet, reconstruction, software.
Note: http://www.cs.rice.edu/~nakhleh/Papers/NWLSjcb.pdf.
       

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Dave MacLeod, Robert L. Charlebois, W. Ford Doolittle and Eric Bapteste. Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement. In BMCEB, Vol. 5(27), 2005.  
Keywords: explicit network, from rooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program HorizStory, reconstruction, software.
Note: http://dx.doi.org/10.1186/1471-2148-5-27.
       
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Robert G. Beiko and Nicholas Hamilton. Phylogenetic identification of lateral genetic transfer events. In BMCEB, Vol. 6(15), 2006.  
Keywords: evaluation, from rooted trees, from unrooted trees, lateral gene transfer, Program EEEP, Program HorizStory, Program LatTrans, reconstruction, software, SPR distance.
Note: http://dx.doi.org/10.1186/1471-2148-6-15.
       
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Daniel H. Huson, Daniel C. Richter, Christian Rausch, Tobias Dezulian, Markus Franz and Regula Rupp. Dendroscope: An interactive viewer for large phylogenetic trees. In BMCB, Vol. 8:460, 2007.  
Keywords: phylogeny, Program Dendroscope, software, visualization.
Note: http://dx.doi.org/10.1186/1471-2105-8-460, slides available at http://www.newton.cam.ac.uk/webseminars/pg+ws/2007/plg/plgw01/0903/huson/, software freely available from http://www.dendroscope.org.
       
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Dan Gusfield, Vikas Bansal, Vineet Bafna and Yun S. Song. A Decomposition Theory for Phylogenetic Networks and Incompatible Characters. In JCB, Vol. 14(10):1247-1272, 2007.  
Keywords: explicit network, from sequences, galled tree, phylogenetic network, phylogeny, Program Beagle, Program GalledTree, recombination, reconstruction, software.
Note: http://www.eecs.berkeley.edu/~yss/Pub/decomposition.pdf.
       

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Patricia Buendia and Giri Narasimhan. Serial NetEvolve: A flexible utility for generating serially-sampled sequences along a tree or recombinant network. In BIO, Vol. 18(22):2313-2314, 2006.  
Keywords: generation, phylogenetic network, phylogeny, Program Serial NetEvolve, Program Treevolve, recombination, software.
Note: http://dx.doi.org/10.1093/bioinformatics/btl387.
       
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Patricia Buendia and Giri Narasimhan. Sliding MinPD: Building evolutionary networks of serial samples via an automated recombination detection approach. In BIO, Vol. 23(22):2993-3000, 2007.  
Keywords: from sequences, phylogenetic network, phylogeny, Program Sliding MinPD, recombination, recombination detection, serial evolutionary networks, software.
Note: http://dx.doi.org/10.1093/bioinformatics/btm413.
       
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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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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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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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Cuong Than, Derek Ruths and Luay Nakhleh. PhyloNet: A Software Package for Analyzing and Reconstructing Reticulate Evolutionary Relationships. In BMCB, Vol. 9(322), 2008.  
Keywords: Program PhyloNet, software.
Note: http://dx.doi.org/10.1186/1471-2105-9-322.
       
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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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Supriya Munshaw and Thomas B. Kepler. An Information-Theoretic Method for the Treatment of Plural Ancestry in Phylogenetics. In MBE, Vol. 25(6):1199-1208, 2008.  
Keywords: explicit network, from sequences, heuristic, phylogenetic network, reconstruction, simulated annealing, software.
Note: http://dx.doi.org/10.1093/molbev/msn066.
       
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Miguel Arenas and David Posada. Recodon: Coalescent simulation of coding DNA sequences with recombination, migration and demography. In BMCB, Vol. 8(458), 2008.  
Keywords: coalescent, generation, Program Recodon, software.
Note: http://dx.doi.org/10.1186/1471-2105-8-458.
       
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29
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Martin Lott, Andreas Spillner, Katharina Huber and Vincent Moulton. PADRE: A Package for Analyzing and Displaying Reticulate Evolution. In BIO, Vol. 25(9):1199-1200, 2009.  
Keywords: duplication, explicit network, from multilabeled tree, phylogenetic network, phylogeny, Program PADRE, reconstruction, software.
Note: http://dx.doi.org/10.1093/bioinformatics/btp133.
       
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30
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Katharina Huber, Leo van Iersel, Steven Kelk and Radoslaw Suchecki. A Practical Algorithm for Reconstructing Level-1 Phylogenetic Networks. In TCBB, Vol. 8(3):607-620, 2011.  
Keywords: explicit network, from triplets, galled tree, generation, heuristic, phylogenetic network, phylogeny, Program LEV1ATHAN, Program Lev1Generator, reconstruction, software.
Note: http://arxiv.org/abs/0910.4067.
       
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Josh Voorkamp né Collins, Simone Linz and Charles Semple. Quantifying hybridization in realistic time. In JCB, Vol. 18(10):1305-1318, 2011.  
Keywords: explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, software.
Note: http://wwwcsif.cs.ucdavis.edu/~linzs/CLS10_interleave.pdf, software available at http://www.math.canterbury.ac.nz/~c.semple/software.shtml.
       
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32
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Miguel Arenas, Mateus Patricio, David Posada and Gabriel Valiente. Characterization of Phylogenetic Networks with NetTest. In BMCB, Vol. 11:268, 2010.  
Keywords: explicit network, galled tree, phylogenetic network, Program NetTest, software, time consistent network, tree child network, tree sibling network, visualization.
Note: http://dx.doi.org/10.1186/1471-2105-11-268, software available at http://darwin.uvigo.es/software/nettest/.
       
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Sophie Abby, Eric Tannier, Manolo Gouy and Vincent Daubin. Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests. In BMCB, Vol. 11:324, 2010.  
Keywords: explicit network, from rooted trees, from species tree, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program EEEP, Program PhyloNet, Program Prunier, reconstruction, software.
Note: http://www.biomedcentral.com/1471-2105/11/324.
       
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Nicolas Galtier. A model of horizontal gene transfer and the bacterial phylogeny problem. In Systematic Biology, Vol. 56(4):633-642, 2007.  
Keywords: explicit network, generation, lateral gene transfer, phylogenetic network, phylogeny, Program HGT_simul, software, statistical model.
Note: http://dx.doi.org/10.1080/10635150701546231.
       
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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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Zhi-Zhong Chen and Lusheng Wang. HybridNET: a tool for constructing hybridization networks. In BIO, Vol. 26(22):2912-2913, 2010.  
Keywords: agreement forest, FPT, from rooted trees, hybridization, phylogenetic network, phylogeny, Program HybridNET, software.
Note: http://rnc.r.dendai.ac.jp/~chen/papers/note2.pdf.
       
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Klaus Schliep. Phangorn: Phylogenetic analysis in R. In Bioinformatics, Vol. 27(4):592-593, 2011.  
Keywords: abstract network, from distances, phylogenetic network, Program Phangorn, software, split, split network.
Note: http://dx.doi.org/10.1093/bioinformatics/btq706.
       
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Steven Kelk, Celine Scornavacca and Leo van Iersel. On the elusiveness of clusters. In TCBB, Vol. 9(2):517-534, 2012.  
Keywords: explicit network, from clusters, from rooted trees, from triplets, level k phylogenetic network, phylogenetic network, phylogeny, Program Clustistic, reconstruction, software.
Note: http://arxiv.org/abs/1103.1834.
       

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Paul Phipps and Sergey Bereg. Optimizing Phylogenetic Networks for Circular Split Systems. In TCBB, Vol. 9(2):535-547, 2012.  
Keywords: abstract network, from distances, from splits, phylogenetic network, phylogeny, Program PhippsNetwork, reconstruction, software.
       
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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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Reza Hassanzadeh, Changiz Eslahchi and Wing-Kin Sung. Constructing phylogenetic supernetworks based on simulated annealing. In MPE, Vol. 63(3):738-744, 2012.  
Keywords: abstract network, from unrooted trees, heuristic, phylogenetic network, phylogeny, Program SNSA, reconstruction, simulated annealing, software, split network.
Note: http://dx.doi.org/10.1016/j.ympev.2012.02.009.
       
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Hadi Poormohammadi, Changiz Eslahchi and Ruzbeh Tusserkani. TripNet: A Method for Constructing Rooted Phylogenetic Networks from Rooted Triplets. In PLoS ONE, Vol. 9(9):e106531, 2014.  
Keywords: explicit network, from triplets, heuristic, level k phylogenetic network, phylogenetic network, phylogeny, Program TripNet, reconstruction, software.
Note: http://arxiv.org/abs/1201.3722.
       
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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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Alix Boc, Alpha B. Diallo and Vladimir Makarenkov. T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks. In NAR, Vol. 40(W1):W573-W579, 2012.  
Keywords: from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, Program T REX, reconstruction, reticulogram, software.
Note: http://dx.doi.org/10.1093/nar/gks485.
       
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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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Zhi-Zhong Chen, Lusheng Wang and Satoshi Yamanaka. A fast tool for minimum hybridization networks. In BMCB, Vol. 13:155, 2012.  
Keywords: agreement forest, explicit network, from rooted trees, phylogenetic network, phylogeny, Program FastHN, reconstruction, software.
Note: http://dx.doi.org/10.1186/1471-2105-13-155.
       
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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.
       

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Fenglou Mao, David Williams, Olga Zhaxybayeva, Maria S. Poptsova, Pascal Lapierre, J. Peter Gogarten and Ying Xu. Quartet decomposition server: a platform for analyzing phylogenetic trees. In BMCB, Vol. 13:123, 2012.  
Keywords: abstract network, from quartets, phylogenetic network, phylogeny, Program Quartet Decomposition, reconstruction, software, split network.
       
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Thi-Hau Nguyen, Vincent Ranwez, Stéphanie Pointet, Anne-Muriel Chifolleau Arigon, Jean-Philippe Doyon and Vincent Berry. Reconciliation and local gene tree rearrangement can be of mutual profit. In ALMOB, Vol. 8(12), 2013.  
Keywords: duplication, explicit network, from rooted trees, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program Mowgli, Program MowgliNNI, Program Prunier, reconstruction, software.
       
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Juan Wang, Maozu Guo, Xiaoyan Liu, Yang Liu, Chunyu Wang, Linlin Xing and Kai Che. LNETWORK: An Efficient and Effective Method for Constructing Phylogenetic Networks. In BIO, Vol. 29(18):2269-2276, 2013.  
Keywords: explicit network, from rooted trees, phylogenetic network, phylogeny, Program LNetwork, reconstruction, software.
       
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Juan Wang, Maozu Guo, Linlin Xing, Kai Che, Xiaoyan Liu and Chunyu Wang. BIMLR: A Method for Constructing Rooted Phylogenetic Networks from Rooted Phylogenetic Trees. In Gene, Vol. 527(1):344-351, 2013.  
Keywords: explicit network, from clusters, from rooted trees, phylogenetic network, phylogeny, Program BIMLR, Program Dendroscope, reconstruction, software.
       
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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.
       

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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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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.
       

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

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

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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.
       

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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.
       

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Claudia Solís-Lemus, Paul Bastide and Cécile Ané. PhyloNetworks: A Package for Phylogenetic Networks. In MBE, 2017.  
Keywords: from sequences, from trees, likelihood, Program PhyloNetworks SNaQ, software.
Note: https://doi.org/10.1093/molbev/msx235, to appear.
       

InProceedings
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Rune Lyngsø, Yun S. Song and Jotun Hein. Minimum Recombination Histories by Branch and Bound. In WABI05, Vol. 3692:239-250 of LNCS, springer, 2005.  
Keywords: ARG, branch and bound, from sequences, minimum number, Program Beagle, recombination, reconstruction, software.
Note: http://www.cs.ucdavis.edu/~yssong/Pub/WABI05-239.pdf.
       

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Luay Nakhleh, Tandy Warnow and C. Randal Linder. Reconstructing reticulate evolution in species - theory and practice. In RECOMB04, Pages 337-346, 2004.  
Keywords: from rooted trees, galled tree, phylogenetic network, phylogeny, polynomial, Program SPNet, reconstruction, software.
Note: http://www.cs.rice.edu/~nakhleh/Papers/144-nakhleh.pdf.
       

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Yufeng Wu. Close Lower and Upper Bounds for the Minimum Reticulate Network of Multiple Phylogenetic Trees. In ISMB10, Vol. 26(12):i140-i148 of BIO, 2010.  
Keywords: explicit network, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program PIRN, software.
Note: http://dx.doi.org/10.1093/bioinformatics/btq198.
       
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Hyun Jung Park and Luay Nakhleh. MURPAR: A fast heuristic for inferring parsimonious phylogenetic networks from multiple gene trees. In ISBRA12, Vol. 7292:213-224 of LNCS, springer, 2012.  
Keywords: explicit network, from unrooted trees, heuristic, phylogenetic network, phylogeny, reconstruction, software.
Note: https://www.researchgate.net/profile/Hyun_Jung_Park2/publication/262318595_MURPAR_A_Fast_Heuristic_for_Inferring_Parsimonious_Phylogenetic_Networks_from_Multiple_Gene_Trees/links/54b7e7b50cf269d8cbf58cc4.pdf.
       
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Leo van Iersel, Steven Kelk, Nela Lekic and Celine Scornavacca. A practical approximation algorithm for solving massive instances of hybridization number. In WABI12, Vol. 7534(430-440) of LNCS, springer, 2012.  
Keywords: agreement forest, approximation, explicit network, from rooted trees, hybridization, phylogenetic network, phylogeny, Program CycleKiller, Program Dendroscope, Program HybridNET, reconstruction, software.
Note: http://arxiv.org/abs/1205.3417.
       
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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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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.
       

MastersThesis
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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.
       

69
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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.
       

PhdThesis
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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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Martin Lott. New Methods for Constructing Phylogenetic Networks from Multi-Labelled Trees. PhD thesis, University of East Anglia, U.K., 2009.  
Keywords: duplication, explicit network, from multilabeled tree, phylogenetic network, phylogeny, Program PADRE, reconstruction, software.
Note: http://www.ic0.net/thesis-martin-final.pdf.
       

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

Misc
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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.
       

74
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Nicholas C. Grassly and Andrew Rambaut. Treevolve, a program to simulate the evolution of DNA sequences under different population dynamic scenarios. 1999.  
Keywords: generation, phylogenetic network, phylogeny, population genetics, Program Treevolve, software.
Note: http://evolve.zoo.ox.ac.uk/software/treevolve/manual.php.
       

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

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

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

79
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Benjamin Albrecht. Computing a Relevant Set of Nonbinary Maximum Acyclic Agreement Forests. 2015.  
Keywords: agreement forest, explicit network, exponential algorithm, from rooted trees, phylogenetic network, phylogeny, Program Hybroscale, reconstruction, software.
Note: http://arxiv.org/abs/1512.05703.
       

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

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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. 2017.  
Keywords: abstract network, NeighborNet, phylogenetic network, phylogeny, Program FlatNJ, Program QNet, Program SplitsTree, reconstruction, software, split network.
Note: https://doi.org/10.1101/169177.