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 (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 maximum 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.
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 1.8 is being used.
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.
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
script.nex is the NEXUS file containing the commands to be executed.
Scoring a candidate species phylogeny
Inferring a species phylogeny
For other tools in PhyloNet, please see here for a full list.
Here is the yeast data set (Rokas et al., 2003) that you could try to analyze using our tools. It consists of 106 loci, each with a single allele sampled from seven Saccharomyces species S. cerevisiae (Scer), S. paradoxus (Spar), S. mikatae (Smik), S. kudriavzevii (Skud), S. bayanus (Sbay), S. castellii (Scas), S. kluyveri (Sklu), and the outgroup fungus Candida albicans (Calb).
The followings are the input NEXUS file you could try:
Phylogenetic network in Rich Newick string can be visualized in Dendroscope. However, Dendroscope can not recognize inheritance probabilities (branch lengths and supports are fine). You have to remove those probabilities manually from the Rich Newick string, or use option "-di" so that PhyloNet returns the network that Dendroscope takes directly. For example, the following network is what PhyloNet returns when the input NEXUS file InferringNetworkMP is used:
In order to visualize this phylogenetic network in Dendroscope, please remove the inheritance probabilities like follows, and Dendroscope will be able to read it. Or you can use option "-di".
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.