Pyvolve Manual

• Introduction
• Installation
• Citation
• Basic Usage
• Defining phylogenies
• Defining Evolutionary Models
  • Nucleotide Models
  • Amino-acid models
  • Mechanistic (dN/dS) codon models
  • Mutation-selection models
  • Empirical codon model
  • Specifying custom rate matrices
  • Specifying equilibrium frequencies
    • EqualFrequencies class
    • RandomFrequencies class
    • CustomFrequencies class
    • ReadFrequencies class
    • EmpiricalModelFrequencies class
    • Restricting frequencies to certain states
    • Converting frequencies between alphabets
  • Specifying mutation rates
• Mutation rates vs. branch lengths
• Defining Partitions
  • Specifying ancestral sequences
• Evolving sequences
  • Evolver output files
  • Sequence post-processing
    • Interpreting the "site_rates.txt" output file
    • Interpreting the "site_rates_info.txt" output file
  • Simulating replicates
• Implementing site-wise rate heterogeneity
  • Implementing site-wise heterogeneity for nucleotide and amino-acid models
    • Gamma-distributed rate categories
    • Custom-distributed rate categories
  • Implementing site-wise heterogeneity for mechanistic codon models
  • Implementing site-wise heterogeneity for mutation-selection models
  • Implementing site-wise heterogeneity for the Empirical Codon Model
• Implementing branch (temporal) heterogeneity
• Implementing branch-site heterogeneity