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Parsimonious:
- inferring a species tree (ILS): InferST_MDC
- inferring a species tree/network (ILS+hybridization): InferNetwork_parsimoniousparsimony
Probabilistic:
- inferring a species tree/network (ILS+hybridization): InferNetwork InferNetwork_probabilisticML

For other tools in PhyloNet, please see here for a full list.

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