PhyloNetworks: A Package for Phylogenetic Networks

Abstract

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.

Keywords: SNaQ; bootstrap; extended Newick; gene flow; hybridization; introgression; network visualization; phylogenetic comparative method.