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Species phylogeny inference is central in biology. PhyloNet considers the scenarios where the incongruence among gene trees are caused by incomplete lineage sorting (ILS) and hybridization (or horizontal gene transfer). More precisely, if assuming ILS is the only cause of gene tree incongruence, then given a set of gene trees, PhyloNet provides tools that can score a candidate species tree as well as infer a species tree under the criterion of minimizing deep coalescence (MDC). On the other hand, if assuming that the incongruence among gene trees are caused by both ILS and hybridization (or horizontal gene transfer), then given a set of gene trees, PhyloNet provides both parsimony-based and probabilistic methods that can score a candidate species network as well as inferring a species networkmaximum parsimony, maximum likelihood, maximum pseudo-likelihood and Bayesian inferences of species networks. Furthermore, if you have some hypothesis of the species networks you want to compare, PhyloNet also provides tools to compute the parsimonious and likelihood score of given species networks.

2. Installation

System Requirements

In order to run the PhyloNet toolkit, you must have Java 1.8.0 or later installed on your system. All references to the java command assume that Java 1.7 8 is being used.

• To check your Java version, type "java -version" on your command line. 
• To download Java 1.8, please go to website http://www.java.com/en/download/.
• To link to the new downloaded Java 1.8, for mac, try these two commands from command line: 
  sudo rm /usr/bin/java 
  sudo ln -s /Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/bin/java /usr/bin

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