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Welcome to the mptp wiki! You will find here more documentation material regarding mptp. Including theoretical background, use cases, option and output explanation.

Theoretical aspects of PTP

mptp command-line options reference

Beginner's guide to mptp

• Input data
  • Pre-processing
  • Tree file and outgroup specification
    • Unique haplotypes
    • Tree inference
    • Estimation of minimum branch length
• Maximum likelihood delimitation
  • Single-rate Poisson tree process
  • Multi-rate Poisson tree processes
  • Likelihood ratio test
    • p-value specification
• Species delimitation using Markov-Chain Monte-Carlo
  • Overview of command-line parameters
  • Output files
  • Examples of convergence
• Support values
  • Posterior probabilities for speciation
  • Posterior probabilities for species most recent common ancestors
  • Average standard deviation of split frequencies
  • Average support of ML tree
• Visualization