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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

  • Input tree
  • Estimation of minimum branch length
  • Outgroup

• Maximum likelihood delimitation

  • Single-rate Poisson tree process
    • Likelihood ratio test
  • Multi-rate Poisson tree processes
    • Multi-Model Comparison
  • Which Model should I use?
  • Usage

• Markov-Chain Monte-Carlo

  • Overview of Command-line Parameters
  • Command line examples
  • Support values and credible intervals
    • Average Support Values (ASV)
    • Average Standard Deviation of Delmitation Support Values (ASDDSV)
    • Credible Intervals
  • 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