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- Count the number of extra lineages given a species tree: parsimoniouslyScoringTree
- Compute the probability of the gene trees given a species tree: probabilisticallyScoringTree
- Infer the species tree using parsimonious method: parsimoniouslyInferringTree
- Infer the species tree using probabilistic method: inferProbabilisticTree probabilisticallyInferringTree
- Count the number of extra lineages given a species network: parsimoniouslyScoringNetwork
- Compute the probability of the gene trees given a species network: probabilisticallyScoringNetwork
- Infer the species network using parsimonious method: parsimoniouslyInferringNetwork
- Infer the species network using probabilistic method: probabilisticallyInferringNetwork
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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