MrBayes: Bayesian Inference of Phylogeny

MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees.

The program takes as input a character matrix in a NEXUS file format. The output is several files with the parameters that were sampled by the MCMC algorithm. MrBayes can summarize the information in these files for the user. The program features include:

• A common command-line interface for Macintosh, Windows, and UNIX operating systems;
• Extensive help available via the command line;
• Ability to analyze nucleotide, amino acid, restriction site, and morphological data;
• Mixing of data types, such as molecular and morphological characters, in a single analysis;
• A general method for assigning 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 Bayes framework;
• The ability to spread jobs over a cluster of computers using MPI (for Macintosh and UNIX environments only).

The most recent version of the program, 3.1, is the first non-beta release of MrBayes 3. Compared to previous beta versions, it includes numerous bug fixes as well as several new features such as topology constraints, inference of ancestral states and site rates, and simultaneous independent runs with convergence diagnostics calculated on the fly.