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 4x4, 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;
* 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 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);
* Check pointing across all models, allowing the user to seamlessly extend a previous analysis or recover from a system crash;