MrBayes is a program used for bayesian inference of phylogeny. MrBayes is cowritten by John Huelsenbeck and Fredrik Ronquist.
The version of MrBayes included with this version of Rocks is MPI enabled, and can be used in either parallel or serial modes of execution.
MrBayes uses the NEXUS file format for input. To use MrBayes in interactive mode, just type mb at the command line
[nostromo@xxx mrbayes]$ mb MrBayes v3.1.2 (Bayesian Analysis of Phylogeny) (Parallel version) (1 processors available) by Fredrik Ronquist and John P. Huelsenbeck School of Computational Science Florida State University ronquist@csit.fsu.edu Section of Ecology, Behavior and Evolution Division of Biological Sciences University of California, San Diego johnh@biomail.ucsd.edu Distributed under the GNU General Public License Type "help" or "help <command>" for information on the commands that are available. MrBayes > |
To use MrBayes in the parallel version, you'll need to use it in non-interactive mode. It can be invoked as shown.
[nostromo@xxx ~]$ /opt/openmpi/bin/mpirun -np 4 /opt/bio/mrbayes/mb /opt/bio/mrbayes/primates.nex > ~/log.txt [nostromo@xxx ~]$ cat log.txt MrBayes v3.1.2 (Bayesian Analysis of Phylogeny) (Parallel version) (4 processors available) by John P. Huelsenbeck and Fredrik Ronquist Section of Ecology, Behavior and Evolution Division of Biological Sciences University of California, San Diego johnh@biomail.ucsd.edu School of Computational Science Florida State University ronquist@csit.fsu.edu Distributed under the GNU General Public License Type "help" or "help <command>" for information on the commands that are available. Executing file "/opt/bio/mrbayes/primates.nex" UNIX line termination Longest line length = 915 Parsing file Expecting NEXUS formatted file Reading data block Allocated matrix Matrix has 12 taxa and 898 characters Data is Dna Data matrix is not interleaved Gaps coded as - Setting default partition (does not divide up characters). Taxon 1 -> Tarsius_syrichta Taxon 2 -> Lemur_catta Taxon 3 -> Homo_sapiens Taxon 4 -> Pan Taxon 5 -> Gorilla Taxon 6 -> Pongo Taxon 7 -> Hylobates Taxon 8 -> Macaca_fuscata Taxon 9 -> M_mulatta Taxon 10 -> M_fascicularis Taxon 11 -> M_sylvanus Taxon 12 -> Saimiri_sciureus Setting output file names to "/opt/bio/mrbayes/primates.nex.run<i>.<p/t>" Successfully read matrix Exiting data block Reached end of file Tasks completed, exiting program because mode is noninteractive To return control to the command line after completion of file processing, set mode to interactive with 'mb -i <filename>' (i is for interactive) or use 'set mode=interactive' [nostromo@xxx ~]$ |
A wealth of information about MrBayes is available at the MrBayes Home Page and at the MrBayes Wiki