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1. Introduction

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

2. Installation

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.

3. Usage

4. Website

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. 

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..
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