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.

 ) high-level description of what will be taught in the workshop

2. Installation

System Requirements

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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. Usage

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

• Parsimonious: 
  
  • ILS for a species tree: DeepCoalCount_tree
  • ILS and hybridization for a species network: DeepCoalCount_network
• Probabilistic:
  
  • ILS and hybridization for a species network: CalGTProb

Inferring a species phylogeny

4. Website

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

5. References

• Than C, Ruths D, Nakhleh L. PhyloNet: A Software Package for Analyzing and Reconstructing Reticulate Evolutionary Relationships. BMC Bioinformatics, 9:322, 2008
• C. Than and L. Nakhleh. Species tree inference by minimizing deep coalescences. PLoS Computational Biology, 5(9):e1000501, 2009.
• Y. Yu, T. Warnow, and L. Nakhleh. Algorithms for MDC-based multi-locus phylogeny inference. Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology (RECOMB), LNBI 6577, 531-545, 2011.
• Y. Yu, T. Warnow, and L. Nakhleh. Algorithms for MDC-based multi-locus phylogeny inference: Beyond rooted binary gene trees on single alleles. Journal of Computational Biology, 18(11):1-18, 2011.
• Y. Yu, J.H. Degnan, and L. Nakhleh. The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection. PLoS Genetics, 8(4):e1002660, 2012.
• Y. Yu, R.M. Barnett, and L. Nakhleh. Parsimonious inference of hybridization in the presence of incomplete lineage sorting. Under review
• Y. Yu and L. Nakhleh. Fast algorithms for reconciliation under hybridization and incomplete lineage sorting. In: arXiv:1212.1909.; 2012. p..