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BEAST

“BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability.” *

Beast is a highly configurable piece of software, that can do many analyses. Your best bet is to work through some tutorials on the BEAST website

PBS

beast.pbs

 #!/bin/sh

 #PBS -N beast  
 #PBS -j oe

 . /usr/modules/init/bash  
 module load beast

 beast yourfile.xml

Or, using environment variables and multiple threads:

beast-threads.pbs

 #!/bin/sh

 #PBS -N beast  
 #PBS -j oe  
 #PBS -l nodes=1:ppn=8

 . /usr/modules/init/bash  
 module load beast

 beast -threads 8 $FILE

Run as

# qsub -v FILE=myfile.xml beast.pbs