MrBayes

Description

MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead,]MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees.

Version

  • 3.1.2

Authorized Users

  • CIRCE account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • SC cluster

Modules

MrBayes requires the following module file to run:

  • apps/mrbayes/3.1.2

Running MrBayes on CIRCE/SC

The MrBayes user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

  • Note on CIRCE: Make sure to run your jobs from your $WORK directory!
  • Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Interactive Mode

MrBayes can be run in an interactive mode from the command line. After loading the module as specified above, simply execute “mb” in the terminal window. This will drop you into the MrBayes interactive shell. Typing “help” will give you a list of MrBayes command options, and typing “quit” will exit the program. More information about how to perform an analysis can be found in the Tutorial section of the manual.

  • Note: Please limit your use of the interactive mode to familiarizing yourself with the commands and quick analyses. Running the interactive mode consumes login node resources shared by all. Please be courteous.

Batch Mode

Alternatively, the parallel version of MrBayes can also be run in batch mode using input redirection. For that you need a text file containing the commands exactly as you would have typed them from the command line. For instance, assume that your data set is in primates.nex and that you want to perform a series of commands to analyse it. You will need a text file similar to the one below (named “mrbayes.in” for this example):

set autoclose=yes nowarn=yes
execute primates.nex
lset nst=6 rates=gamma
mcmc ngen=10000 savebrlens=yes file=primates.nex1
mcmc file=primates.nex2
mcmc file=primates.nex3
quit

To submit the job to CIRCE/SC using the “mrbayes.in” sample input file above (and the file “primates.nex” file from the known tests directory below), you would set up a submit script like this:

  • The script below (for testing, name it “mrbayes-test.sh”) can be copied into your job directory (the folder with your input files) and modified so that you can submit batch processes to the queue.
#!/bin/bash
#
#SBATCH --comment=mrbayes-test
#SBATCH --ntasks=4
#SBATCH --job-name=mrbayes-test
#SBATCH --output=output.%j.mrbayes-test
#SBATCH --time=01:00:00

#### SLURM 4 processor MrBayes test to run for 1 hour.

module load apps/mrbayes/3.1.2
mpirun mb_parallel < mrbayes.in > outfile.txt

 
Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./mrbayes-test.sh

Documentation

Home Page, User Guides, and Manuals

Benchmarks, Known Tests, Examples, Tutorials, and Other Resources

  • MrBayes Examples
    • /opt/apps/mrbayes/3.1.2/examples

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with MrBayes to the IT Help Desk: rc-help@usf.edu