Phylogenetic Networks Toolkit



Thank you for your interest in PhyloNet. This software package is developed and maintained by the BioInformatics Group at the Department of Computer Science at Rice University. PhyloNet is aimed mainly at providing a suite of tools for reconstructing and analyzing reticulate (non-treelike) evolutionary relationships. In particular, the software package includes features for inferring horizontal gene transfer from a pair of species/gene trees, and detecting interspecific recombination breakpoints in a sequence alignment. Further, it has the capabilities for reading/storing phylogenetic networks, and comparing phylogenetic networks topologies. As the algorithms for phylogenetic network reconstruction and evaluation make use of algorithmic techniques from the domain of phylogenetic trees, the package also contains several tree-oriented features, such as modules for computing the maximum agreement subtrees, the Robinson-Foulds distance measures, etc.

This work is supported in part by a National Science Foundation grant (CCF-0622037), a Department of Energy grant (DE-FG02-06ER25734), and grant R01LM009494 from the National Library of Medicine. The contents are solely the responsibility of the authors and do not necessarily represent the official views of the DOE, NSF, National Library of Medicine or the National Institutes of Health.

PhyloNet is developed entirely in Java, making it platform independent. To obtain a copy of the tool, download the most recent version from the Downloads section below. Installation and usage instructions can be found in the User Documentation associated with the release downloaded.

You may also be interested in the NEPAL tool for phylogenetic network reconstruction and evaluation using the maximum parsimony (MP) and maximum likelihood (ML) criteria.

The PhyloNet software package is currently under heavy development and improvements (including a GUI, and a myriad of new features); once these are done, the whole package will be made available in open-source. If you would like to report bugs, comments, or questions, please contact us or fill out our feedback survey.

Features that are currently implemented in PhyloNet include:

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If you have not done so already, please take a moment to register with us.

Phylonet Version 2.4

Matlab code for simulating gene trees under the phylogenetic network model in the Yu et al. Syst Biol 2010 paper (.m file)

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JavaDoc for PhyloNet 2.4.

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If you use the PhyloNet tool, please cite:

C. Than, D. Ruths, and L. Nakhleh, "PhyloNet: A Software Package for Analyzing and Reconstructing Reticulate Evolutionary Relationships." BMC Bioinformatics, 9:322, 2008.

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Once you have had the opportunity to try out PhyloNet, please aid us in improving it by answering our brief survey. Your responses help us decide what aspects of PhyloNet deserve the most attention.

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PhyloNet Version 2.4

Release Date: 5/31/2011

New features are added, including refining and rooting gene trees with respect to given species trees under MDC criterion, inferring species trees using bootstrap with existing method. Some bugs in v2.3 are fixed.

PhyloNet Version 2.3

Release Date: 11/09/2010

Fix some bugs in the previous version. New features for MDC are added.

PhyloNet Version 2.2

Release Date: 9/21/2010

The new species inference tools are now available from the graphical interface as well as from the command-line. Bugs with the graphical interface have also been fixed.

PhyloNet Version 2.1

Release Date: 12/10/2009

The package now contains more methods to infer species trees, including MDC, MDC with time, GLASS, extended Majority Consensus. They are included in infer_st tool. Details are described in user manual. New features are only available from command line, not GUI now.

PhyloNet Version 2.0

Release Date: 11/9/2009

The package now includes a graphical user interface, which provides easier access to most of the command-line functionality. A new chapter in the user manual explains the basics of the new interface.

PhyloNet Version 1.7

Release Date: 10/18/2009

The DP tool for inferring species trees from multiple gene trees now can handle multiple-allele gene trees, as well as non-binary gene trees.

Release Date: 06/15/2009

The package contains a new tool for inferring the species tree from gene trees using the MDC criterion. The new tool uses dynamic programming for species tree inference, and CPLEX is not needed.

PhyloNet Version 1.6

Release Date: 12/12/2008

The package contains a bug fix in the tool for inferring the species from gene trees despite lineage sorting.

Release Date: 10/20/2008

The package now has a tool to infer the species tree from gene trees despite lineage sorting.

PhyloNet Version 1.5

Release Date: 07/04/2008

The package now accepts trees with both the distances and bootstrap values (see the manual for more details).

Release Date: 05/24/2008

The tool RiataHgt in Phylonet version 1.5 can now output networks in both formats: eNewick and the edge-list format. After computing HGT events for a set of gene trees, RiataHgt now offers a consensus network in the edge-list format.

Release Date: 02/28/2008

Phylonet version 1.5 now comes with a capability to visualize HGT events.

Release Date: 12/19/2007

PhyloNet version 1.5 includes a new tool for generating a mixed integer linear programming formula that can be solved by CPLEX. The new tool thus allows the user to reconstruct the species tree from a large dataset by using a highly efficient CPLEX program.

PhyloNet Version 1.4

Release Date: 08/17/2007

PhyloNet version 1.4 allows the tool Riata-HGT to evaluate the confidence (or bootstrap) of events it computes. The method for obtaining bootstrap values of events is still under ongoing refinement. You can get the latest stable verion of PhyloNet without event bootstrap here.

PhyloNet Version 1.3

Release Date: 08/03/2007

PhyloNet version 1.3 implements new techniques for handling caterpillars in trees, thus significantly reducing running time for computing HGT.

PhyloNet Version 1.2

Release Date: 10/30/2006

The new release comes with a set of sample input files, and a README file that illustrates the use of different tools with these input files. The tool Riata-HGT was also modified to run on files that contains a species tree and one or more gene trees. Further, the package now includes the COUNTCOAL utility, which enumerates all valid coalescent scenarios of a gene within the branches of a species tree (both species and gene trees are givens as input).

Release Date: 10/9/2006

The tool Riata-HGT is modified and extended to find more solutions and to run more efficiently. Events detected by Riata-HGT are now grouped by components, so that they are easier to analyze. The tool for characterizing phylogenetic networks in terms of tripartitions has also been corrected.

Release Date: 8/29/2006

The tool now allows for scoring the parsimony of phylogenetic networks given sequences at their leaves. The current implementation allows only for Hamming distances (i.e., the distance between two equal-length sequences is the number of positions in which they differ). Weighted Hamming distances, allowing also for different substitution matrices, will be implemented in the future.

PhyloNet Version 1.1

Release Date: 8/25/2006

This release adds support for phylogenetic networks. The package contains tools for reading and writing phylogenetic networks in the eNewick format. It also has tools for characterizing networks (i.e., computing clusters, trees, and tripartitions contained in a network), and for computing the distance between two networks.

PhyloNet Version 1.0

Release Date: 8/21/2006

This release has the same functionality as found in Sequoia Version 1.1.2. The two packages have been merged in order to provide additional support for phylogenetic networks in the near future.

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