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
System Requirements
In order to run the PhyloNet toolkit, you must have Java 1.6.0 or later installed on your system. All references to the java command assume that Java 1.6 is being used.
Downloading phylonet.jar
Acquire the current release of PhyloNet by downloading the most recent version of the PhyloNet JAR file. You will have a file named PhyloNet_X.Y.Z.jar, where X is the major version number and Y and Z are the minor version numbers.
Installing the file
Place the jar file in the desired installation directory. The remainder of this document assumes that it is located in $PHYLONET PATH/jar. Installation is now complete. In order to run PhyloNet, you must execute the file PhyloNet_X.Y.Z.jar, as described in the next section.
Basic Usage
The PhyloNet tool is executed by typing the following command into your console:
>java -jar $PHYLONET PATH/jar/PhyloNet_X.Y.Z.jar script.nex |
Where script.nex is the NEXUS file containing the commands to be executed.
Scoring a candidate species phylogeny
Inferring a species phylogeny
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.