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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
5. Visualizing a Phylogenetic Network
Phylogenetic network in Rich Newick string can be visualized in Dendroscope. However, Dendroscope can not recognize inheritance probabilities (branch lengths and supports are fine). You have to remove those probabilities manually from the Rich Newick string. For example, the following network is what PhyloNet returns when the input NEXUS file InferringNetworkMP is used:
| Code Block |
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((((((Skud,(Sbay)#H1:::0.36082474226804123),((Spar,Scer),Smik)),#H1:::0.6391752577319587),Scas),Sklu),Calb); |
In order to visualize this phylogenetic network in Dendroscope, please remove the inheritance probabilities like follows, and Dendroscope will be able to read it.
| Code Block |
|---|
((((((Skud,(Sbay)#H1),((Spar,Scer),Smik)),#H1,Scas),Sklu),Calb); |
6. Tutorial
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7. 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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8. 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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