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;