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PhyloNet is a tool designed mainly for analyzing, reconstructing, and evaluating reticulate (or non-treelike) evolutionary relationships, generally known as phylogenetic networks. Various methods that we have developed make use of techniques and tools from the domain of phylogenetic trees, and hence the PhyloNet package includes several tools for phylogenetic tree analysis. PhyloNet is released under the GNU General Public License. For the full license, see the file GPL.txt included with this distribution.

 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. Precisely, if 

 

2. Installation

System Requirements

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Scoring a candidate species phylogeny

  • Parsimonious: 
  • Probabilistic:
    • ILS and hybridization for scoring a species tree/network (ILS+hybridization): CalGTProb

Inferring a species phylogeny

  • Parsimonious:
    • inferring a species tree (ILS): Infer_ST_MDC
    • inferring a species tree/network (ILS+hybridization): TBA
  • Probabilistic:
    • inferring a species tree/network (ILS+hybridization): TBA

For other tools in PhyloNet, please see here for a full list.

 

4. Website

To see a full description of PhyloNet, please visit its website, where you can get the latest version of PhyloNet as well as detailed descriptions of all available commands. 

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