PhyloNetworks: A Package for Phylogenetic Networks

PhyloNetworks is a Julia package for the inference, manipulation, visualization, and use of phylogenetic networks in an interactive environment. Inference of phylogenetic networks is done with maximum pseudolikelihood from gene trees or multi-locus sequences (SNaQ), with possible bootstrap analysis....

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Bibliographic Details
Published in:	Molecular biology and evolution Vol. 34; no. 12; pp. 3292 - 3298
Main Authors:	Solís-Lemus, Claudia, Bastide, Paul, Ané, Cécile
Format:	Journal Article
Language:	English
Published:	United States Oxford University Press (OUP) 01-12-2017
Subjects:	Computer Science Life Sciences Mathematics gene flow phylogenetic comparative method extended Newick network visualization bootstrap hybridization SNaQ introgression
Online Access:	Get full text
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Description
Summary:	PhyloNetworks is a Julia package for the inference, manipulation, visualization, and use of phylogenetic networks in an interactive environment. Inference of phylogenetic networks is done with maximum pseudolikelihood from gene trees or multi-locus sequences (SNaQ), with possible bootstrap analysis. PhyloNetworks is the first software providing tools to summarize a set of networks (from a bootstrap or posterior sample) with measures of tree edge support, hybrid edge support, and hybrid node support. Networks can be used for phylogenetic comparative analysis of continuous traits, to estimate ancestral states or do a phylogenetic regression. The software is available in open source and with documentation at https://github.com/crsl4/PhyloNetworks.jl.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	0737-4038 1537-1719
DOI:	10.1093/molbev/msx235