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• Parsimonious:
  
  • inferring a species tree (ILS): InferST_MDC
  • inferring a species tree/network (ILS+hybridization): TBAInferNetwork_parsimonious
• Probabilistic:
  
  • inferring a species tree/network (ILS+hybridization): TBA InferNetwork_probabilistic

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

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• Count the number of extra lineages given a species tree: parsimonyScoringTree parsimoniouslyScoringTree
• Compute the probability of the gene trees given a species tree: probabilisticScoringTreeprobabilisticallyScoringTree
• Infer the species tree using parsimonious method:  inferParsimoniousTree parsimoniouslyInferringTree
• Infer the species tree using probabilistic method: TBAinferProbabilisticTree
• Count the number of extra lineages given a species network: parsimonyScoringNetworkparsimoniouslyScoringNetwork
• Compute the probability of the gene trees given a species network: probabilisticScoringNetworkprobabilisticallyScoringNetwork
• Infer the species network using parsimonious method: TBAparsimoniouslyInferringNetwork
• Infer the species network using probabilistic method: TBAprobabilisticallyInferringNetwork

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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