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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.
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Tutorial
Tutorial pdf 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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