Publications related to 'Program PhyloNet' : PhyloNet is aimed mainly at providing a suite of tools for reconstructing and analyzing reticulate (non-treelike) evolutionary relationships. In particular, the software package includes features for inferring horizontal gene transfer from a pair of species/gene trees, and detecting interspecific recombination breakpoints in a sequence alignment. Further, it has the capabilities for reading/storing phylogenetic networks, and comparing phylogenetic networks topologies. http://bioinfo.cs.rice.edu/phylonet/index.html
 
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Article (Journal)
1
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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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2
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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.
       

3
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Cuong Than, Derek Ruths, Hideki Innan and Luay Nakhleh. Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions. In JCB, Vol. 14(4):517-535, 2007.
Keywords: counting, explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, Program LatTrans, Program PhyloNet.
Note: http://www.cs.rice.edu/~nakhleh/Papers/recombcg06-jcb.pdf.
       

4
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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: agreement forest, explicit network, from rooted trees, from species tree, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program EEEP, Program PhyloNet, Program Prunier, reconstruction, software.
Note: http://www.biomedcentral.com/1471-2105/11/324.
       
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5
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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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6
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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.
       

7
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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.
       

8
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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.
       

9
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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.
       

10
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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.
       

11
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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.
       

InProceedings
12
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Luay Nakhleh, Derek Ruths and Li-San Wang. RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer. In COCOON05, Vol. 3595:84-93 of LNCS, springer, 2005.
Keywords: from rooted trees, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program PhyloNet.
Note: http://www.cs.rice.edu/~nakhleh/Papers/COCOON05.pdf.
       

13
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Cuong Than, Derek Ruths, Hideki Innan and Luay Nakhleh. Identifiability Issues in Phylogeny-Based Detection of Horizontal Gene Transfer. In Proceedings of the Fourth RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG'06), Vol. 4205:215-229 of LNCS, springer, 2006.
Keywords: explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, Program LatTrans, Program PhyloNet.
Note: http://www.cs.rice.edu/~nakhleh/Papers/recombcg06-final.pdf.
       

14
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Cuong Than and Luay Nakhleh. SPR-based Tree Reconciliation: Non-binary Trees and Multiple Solutions. In APBC08, Pages 251-260, 2008.
Keywords: evaluation, from rooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program LatTrans, Program PhyloNet, reconstruction, SPR distance.
Note: http://www.cs.rice.edu/~nakhleh/Papers/apbc08.pdf.
       

15
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Cuong Than, Guohua Jin and Luay Nakhleh. Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer. In Proceedings of the Sixth RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG'08), Vol. 5267:113-127 of LNCS, springer, 2008.
Keywords: bootstrap, explicit network, from rooted trees, from sequences, lateral gene transfer, phylogenetic network, phylogeny, Program Nepal, Program PhyloNet, reconstruction.
Note: http://www.cs.rice.edu/~nakhleh/Papers/recombcg-08.pdf, slides available at http://igm.univ-mlv.fr/RCG08/RCG08slides/Cuong_Than_RCG08.pdf.
       

16
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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.
       

17
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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.
       

InBook
18
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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
       

MastersThesis
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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.
       

PhdThesis
20
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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
21
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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.
       

22
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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.