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- ILS:
- Score a species tree:
- Count the number of extra lineages given a species tree: ScoringTreeUnderParsimony
- Compute the probability of the gene trees given a species tree: ScoringTreeUnderLikelihood
- Infer a species tree:
- Infer the species tree under parsimony: InferringTreeMP
- Infer the species tree using maximum likelihood: InferringTreeML
- Score a species tree:
- ILS + introgression
- Score a species network:
- Count the number of extra lineages given a species network: ScoringNetworkUnderParsimony
- Compute the probability of the gene trees given a species network: ScoringNetworkUnderLikelihood
- Infer a species network:
- Infer the species network under parsimony: InferringNetworkMP
- Infer the species network using maximum likelihood: InferringNetworkML
- Infer the species network using maximum pseudo-likelihood: InferringNetworkMPL
- Infer the species network using Bayesian: InferringNetworkMCMC
- Infer the species network using Bayesian from multilocus data:
- Score a species network:
5. Visualizing a Phylogenetic Network
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