1. Introduction
PhyloNet is a collection of tools 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 1.5.0 or later installed on your system. All references to the java command assume that Java 1.5 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.
3. Basic Usage
The PhloNet 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. Basic NEXUS Overview
When PhyloNet is invoked with a specified NEXUS script file the tool will execute all of the commands contained within the file's PHYLONET
block. For example, consider the following NEXUS file:
#NEXUS BEGIN NETWORKS; Network net = ((a,(b,(c)x#1)),((x#1,d),e)); Network net1 = ((a,(b,(c)x#1)),((d,x#1),e)); Network net2 = ((((a, (c)x#1), d), (b, x)), e); Network net3 = ((a,b),(c,(d,(e,(f,g))))); Network net4 = ((f,b),(c,(d,(a,(e,g))))); END; BEGIN PHYLONET; Charnet net -m tree; Cmpnets net1 net2 -m cluster; CountCoal net3 net4; END;