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Scoring a candidate species phylogeny

• Parsimonious: 
  
  • scoring Scoring a species tree (ILS): DeepCoalCount_tree
  • scoring Scoring a species tree/network (ILS+hybridizationintrogression): DeepCoalCount_network
• Probabilistic:
  
  • scoring Scoring a species tree/network (ILS+hybridizationintrogression): CalGTProb

Inferring a species phylogeny

• ParsimoniousMaximum parsimony:
  
  • inferring Inferring a species tree (ILS): Infer_ST_MDC, Infer_ST_MDC_UR
  • inferring Inferring a species tree/network (ILS+hybridizationintrogression): InferNetwork_MP
• ProbabilisticMaximum likelihood:
  
  • inferring Inferring a species tree/network (ILS+hybridizationintrogression): InferNetwork_ML
  • inferring a species tree/network (ILS+hybridizationintrogression) with cross-validation: InferNetwork_ML_CV
• Maximum pseudo-likelihood:
  
  • Inferring a species tree/network (ILS+introgression): InferNetwork_MPL
• Bayesian:
  
  • Inferring a species tree/network (ILS+introgression): MCMC_GT

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

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The followings are the input NEXUS file you could try:

• 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
• 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
      
      

5. Visualizing a Phylogenetic Network

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