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- Count the number of extra lineages given a species tree: parsimoniouslyScoringTree ScoringTreeUnderParsimony
- Compute the probability of the gene trees given a species tree: probabilisticallyScoringTreeScoringTreeUnderLikelihood
- Infer the species tree using parsimonious method: parsimoniouslyInferringTreeunder parsimony: InferringTreeMP
- Infer the species tree using probabilistic methodusing maximum likelihood: probabilisticallyInferringTree InferringTreeML
- Count the number of extra lineages given a species network: parsimoniouslyScoringNetworkScoringNetworkUnderParsimony
- Compute the probability of the gene trees given a species network: probabilisticallyScoringNetworkScoringNetworkUnderLikelihood
- Infer the species network using parsimonious methodunder parsimony: parsimoniouslyInferringNetwork InferringNetworkMP
- Infer the species network using probabilistic methodmaximum likelihood: probabilisticallyInferringNetwork InferringNetworkML
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.
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