Bioinformatics Applications MrBayes - Bayesian inference of phylogeny using MCMC

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MrBayes is a program for Bayesian inference of phylogeny using Markov Chain Monte Carlo methods. MrBayes has a console interface and uses a modified NEXUS format for data and batch files. It handles a wide range of probabilistic models for the evolution of nucleotide and aminoacid sequences, restriction sites, and standard binary data. The user can set the priors used for the parameters and search for trees under topological constraints. The behavior of the Markov chain can be controlled by setting proposal probabilities for different move types and by invoking heated chains (Metropolis Coupling) to improve performance for difficult problems. Various options are available for summarizing the posterior distribution of the model parameters, including topology and branch lengths, and drawing inferences about ancestral states and site rates.

To start MrBayes type: 'mb' on the command line.

At the MrBayes> prompt type 'help' or 'help command-name' for help.

Detailed description of mrbayes