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- Parsimonious:
- inferring a species tree (ILS): Infer_ST_MDC, Infer_ST_MDC_UR
- inferring a species tree/network (ILS+hybridization): InferNetwork_parsimony
- Probabilistic:
- inferring a species tree/network (ILS+hybridization): InferNetwork_ML
- inferring a species tree/network (ILS+hybridization) with cross-validation: InferNetwork_ML_CV
For other tools in PhyloNet, please see here for a full list.
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