MrBayes

Version

V. 3.1.2 and 3.2 (build 415) installed on HIPPU

V. 3.1.2 and 3.2 (build 415) installed on MURSKA

V. 3.1.2 and 3.2 (build 415) installed on VUORI

Note on versions:

Version 3.1.2 is the latest official stable release. It is, however, rather old and the code has some incompatibility problems with 64 bit systems.  On particular data sets the summary commands (sump, sumt) crash the 64-bit program. We recommend running the 32 bit version (mb32). You can also run the analysis with 64 bit version and just run the summary commands using the 32 bit version.

Version 3.2 is the development version. At least some of the problems with the old version have been fixed, but it's possible that other problems have been introduced. Please inform us if you encounter any problems with it.

In most cases we recomend runing the latest stable release: 32 bit version 3.1.2 (mb32)

Description

MrBayes is a program for the Bayesian inference on phylogenies.

Usage

On all machines MrBayes needs to be initialized before use. This is done with command

module load mrbayes

Version 3.1.2 is loaded by default, but you can specify the version required (use command "module avail" to see available versions):

module load mrbayes/3.2-dev

After loading the module the program (32 bit version) starts with the command (32 bit version only available on version 3.1.2)

mb32

64 bit version starts with command

mb64

Parallel version of that start with the command

mb64par

Note that sometimes on particular data sets MrBayes v 3.1.2 summary commands (sump, sumt) crash the 64-bit program. If this happens, run the analysis (or just the summary) on 32 bit version.

MrBayes takes a character matrix, e.g., DNA sequence alignment, as an input only, if the file is in Nexus-format. Hint: You can save nexus-formatted alignments using, e.g. ClustalX (installed in Hippu).

Batch jobs in Murska

Running MrBayes analysis might take considerable amount of CPU time and memory. To submit a long MrBayes run, you must construct a command file that includes queue options and setup and execution commands for MrBayes. First, note the commands you give to MrBayes in order to perform the analysis, i.e., run MrBayes interactive, and note the commands and the order of the commands you give. Then modify the following batch file accordingly.

#!/bin/csh
#BSUB -L /bin/csh
#BSUB -e mrb1M_err_%J
#BSUB -o mrb1M_out_%J
#BSUB -M 4194304
#BSUB -W 168:00
#BSUB -n 1

mb64 <<EOF
log start filename=data.log
execute cox1.nex
mcmcp ngen=10000
mcmc
no
sump
sumt burnin=250
quit
EOF

You can send the job to execution using the command bsub < batch. Note that all the data files and the batch job file need to be in the $WRKDIR, since computational nodes do not see the home or metawork directories.

Parallel batch jobs in Murska

To run run parallel MrBayes, you'll need three file: batch job file (here, mb64batch), MrBayes command file (here, mbcom), and your data (here, ratite.nxs).

Batch job file, modify this to your liking:

#!/bin/csh
#BSUB -n 4
#BSUB -W 2:00
#BSUB -o mpi_mrbayes.out.%J
#BSUB -M 1048576
#BSUB -N
#BSUB -u your.email@anywhere.fi

mpirun -srun mb64par < mbcom > log.txt

MrBayes command file (mbcom) should include all the command you would type in MrBays in interactive mode, also:

execute ratite.nxs
mcmcp ngen=10000
mcmc
no
sump
sumt
quit

Manual

A detailed description of MrBayes commands is found in the manual.

You might also want to read the worked-out examples in Molecular systematics - material for practicals.

Distribution

MrBayes can be downloaded from it's website.

User support