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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
