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MrBayes: Bayesian Inference of Phylogeny

Bug Report
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 partitions;
  • An abundance of evolutionary models, including 4 X 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 coalescent.
  • 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 format;
  • 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);
  • Checkpointing across all models, allowing the user to seemlessly extend a previous analysis or recover from a system crash;