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Using Mr. Bayes on the CCLS HPC Dell Cluster

Versions of Mr. Bayes Installed on the CCLS Cluster

Mr. Bayes has been compiled for LAM/MPI use.

Using mb

Interactively

sh UNIX Shell Command Example interactive usage of mb
[mikewong @ccls ~]$ mb


                               MrBayes v3.1.2

                      (Bayesian Analysis of Phylogeny)

                                     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 " for information
                     on the commands that are available.


MrBayes >

As a Non-Interactive Batch Process

sh UNIX Shell Command Example non-interactive usage of mb
[mikewong @ccls ~]$ export PREFIX=/home/mikewong/research/spicerlab/mrbayes

[mikewong @ccls ~]$ bsub -N -u mikewong@sfsu.edu \
> -o $PREFIX/xerula-lava.out \
> -e $PREFIX/xerula-lava.err \
> mb $PREFIX/Xerula.nex

A script has been written to simplify this process:

sh UNIX Shell Command Recommended non-interactive usage of mb
[mikewong @ccls ~]$ lava-mb -u mikewong@sfsu.edu Xerula.nex
Last revised: r2 - 11 Mar 2009 - 23:58:25 - Mike Wong
 
Center for Computing for Life Sciences
San Francisco State University
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