Table of Contents

• Introduction
  • Why is PHASE different from other phylogenetic programs?
  • Acknowledgements
  • How to read this manual ?
  • Aquiring and installing the software
    • MS-Windows installation
    • Unix-like system installation
  • Description of programs in the PHASE package
    • optimise and mlphase
    • mcmcphase and consensus
    • likelihood
    • simulate
    • analyser
  • Running the programs
  
  
• Using programs in the PHASE package
  • Inputs/outputs in PHASE
    • Data file format
      • File content
      • Pairing mask
      • Molecular sequences
      • Class section
    • Control file format
    • Tree file format
    • Substitution model parameters file format
      • Model parameters file content
      • Producing a model parameters file
    • Parameters displayed on the screen and output of each program
    • Clade file format
  • Control files
    • Structure of the control files
    • Datafile block
    • Model block
      • Simple substitution model
      • Mixed model for combined analyses of heterogeneous data
  • Using the programs in the PHASE package
    • likelihood
      • Using likelihood
      • Control file for likelihood
    • optimise
      • Using optimise
      • Control file for optimise
    • simulate
      • Using simulate
      • Control file for simulate
    • mlphase
      • Using mlphase
      • Control file for mlphase
    • mcmcphase
      • Using mcmcphase
      • Using consensus
      • Control file for mcmcphase
      • PERTURBATION block
      • PERTURBATION Block for MIXED models
      • Proposals priority
    • analyser
  
  
• Elements of phylogenetic theory
  • Phylogenetic trees
    • Unrooted phylogenies
    • String representation of a tree
    • Branch lengths
  • Nucleotide substitution models
    • A Markov model of substitution
    • Transition matrices
    • Nucleotide substitution models implemented in PHASE
      • JC69 model (Jukes-Cantor, 69)
      • K80 model (Kimura, 80)
      • HKY85 model (Hasegawa-Kishino-Yano, 85)
      • TN93 model (Tamura-Nei, 93)
      • REV model (Yang, 94)
  • Paired-site substitution models
    • RNA secondary structure
    • Theory of compensatory substitutions
    • Base-paired substitution models implemented in PHASE
      • RNA6A model
      • RNA6B model (Tillier, 94)
      • RNA7A model
      • RNA7D model (Tillier, 98)
      • RNA16A model
  • Refinements to substitution models
    • Invariant and discrete gamma models
    • The MIXED model
  • Bayesian phylogenetics
    • Bayes' theorem
    • Markov chain Monte-Carlo (MCMC)
    • Priors and proposals
      • Uniform priors ?
      • Proposals for the parameters
      • Proposals for the tree
    • Pitfalls of Markov chain Monte-Carlo techniques