1. Introduction
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.
1.1 Contributors
PhyloNet is designed, implemented, and maintained by Rice's BioInformatics Group, which is lead by Professor Luay Nakhleh (nakhleh@cs.rice.edu). For more details related to this group please visit http://bioinfo.cs.rice.edu.
2. Installation
System Requirements
In order to run the PhyloNet toolkit, you must have Java 1.7.0 or later installed on your system. All references to the java command assume that Java 1.7 is being used.
- To check your Java version, type "java -version" on your command line.
- To download Java 1.7, please go to website http://www.java.com/en/download/.
- To link to the new downloaded Java 1.7, 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
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.
3. 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.
4. Illustrating the Various Inference Methods in PhyloNet
4.1 Inference Under the MDC Criterion
| Input nexus file |
|---|
| InferNetwork_MP_0_true.nex |
| InferNetwork_MP_1_true.nex |
| InferNetwork_MP_2_true.nex |
| InferNetwork_MP_3_true.nex |
| InferNetwork_MP_4_true.nex |
Corresponding results: Fig 4 in section 4.1
4.2 Maximum Likelihood Inference