...

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 . Precisely, if (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 both parsimony-based and probabilistic methods that can score a candidate species network as well as inferring a species network.

2. Installation

System Requirements

...

• Parsimonious:
  
  • inferring a species tree (ILS): Infer_ST_MDC
  • inferring a species tree/network (ILS+hybridization): TBA
• Probabilistic:
  
  • inferring a species tree/network (ILS+hybridization): TBA

For other tools in PhyloNet, please see here for a full list.

4. Yeast Data Set

Here is the yeast data set that you could try: yeast.

5. 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. 

...

6. 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..