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.
The program is authored by John P. Huelsenbeck (Dept. Biology, University of Rochester) and Fredrik Ronquist (Evolutionary Biology Centre, Uppsala University).
To start MrBayes on the zisgi you just have to type
nobody@zisgi % mb
on the command line.
Sample Nexus files are in: /usr/local/src/biocomputing/mb_2.01
The following Sample-NEXUS-files are available and downloadable:
Documentation:
MrBayes: Bayesian inference of phylogeny