MrBayes | index

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MrBayes | index

Vetenskapsradet Naturhistoriska Riksmuseet National Bioinformatics Infrastructure Sweden (NBIS)
National Institutes of Health National Science Foundation

MrBayes is a program for Bayesian inference and model choice
across a wide range of phylogenetic and evolutionary models.
MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate
the posterior distribution of model parameters.

Program features include:

  • A common command-line interface across Macintosh, Windows,
    and UNIX operating systems;
  • Extensive help available from the command line;
  • Analysis of nucleotide, amino acid, restriction site, and
    morphological data;
  • Mixing of data types, such as molecular and morphological
    characters, in a single analysis;
  • Easy linking and unlinking of parameters across data
  • An abundance of evolutionary models, including 4×4, doublet,
    and codon models for nucleotide data and many of the standard
    rate matrices for amino acid data;
  • Estimation of positively selected sites in a fully
    hierarchical Bayesian framework;
  • Full integration of the BEST algorithms for the multi-species
  • Estimation of time calibrated (clock) trees using a variety
    of (strict and) relaxed-clock models;
  • Support for complex combinations of positive, negative, and
    backbone constraints on topologies;
  • Model jumping across the GTR model space and across fixed
    rate matrices for amino acid data;
  • Monitoring of convergence during the analysis, and access to
    a wide range of convergence diagnostics tools after the analysis
    has finished;
  • Rich summaries of posterior samples of branch and node
    parameters printed to majority rule consensus trees in FigTree
  • Implementation of the stepping-stone method for accurate
    estimation of model likelihoods for Bayesian model choice using
    Bayes factors;
  • The ability to spread jobs over a cluster of computers using
    MPI (for Macintosh (OS X) and UNIX environments only);
  • Support for the BEAGLE library, resulting in dramatic
    speedups for codon and amino acid models on compatible hardware
    (NVIDIA graphics cards);
  • Check pointing across all models, allowing the user to
    seamlessly extend a previous analysis or recover from a system

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