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- Count the number of extra lineages given a species tree: ScoringTreeUnderParsimony
- Compute the probability of the gene trees given a species tree: ScoringTreeUnderLikelihood
- Infer the species tree under parsimony: InferringTreeMP
- Infer the species tree using maximum likelihood: InferringTreeML
- Count the number of extra lineages given a species network: ScoringNetworkUnderParsimony
- Compute the probability of the gene trees given a species network: ScoringNetworkUnderLikelihood
- Infer the species network under parsimony: InferringNetworkMP
- Infer the species network using maximum likelihood: InferringNetworkML
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5. Website
Tutorial pdf
6. 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.
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7. References
- . 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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