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MrBayes

module avail mrbayes/

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.

Usage

Basic steps

There are four steps to a typical Bayesian phylogenetic analysis using MrBayes:

  1. Read the Nexus data file
  2. Set the evolutionary model
  3. Run the analysis
  4. Summarize the samples

Example

The common begin of nex file for analysis is

#NEXUS
[saved by seaview on Wed Oct 26 08:34:48 2011]
BEGIN DATA;
  DIMENSIONS NTAX=52 NCHAR=1153;
  FORMAT DATATYPE=DNA
  GAP=-
  ;
MATRIX
[1] TCCMP1185
cgaaagcctgacggagca...

and the end of file

...cctcctt
;
begin mrbayes;



    [ Set the parameters of the likelihood model, keeping prset at default conditions ]
    lset 
        nst=6
        nucmodel=4by4
        code=universal
        rates=gamma
        ngammacat=4;

    [ Set the outgroup for the analysis ]
    outgroup 52;

    [ Set Markov chain Monte Carlo parameters ]
    mcmcp
        ngen=50000
        nruns=2
        swapfreq=5
        printfreq=100
        samplefreq=100
        nchains=4
        savebrlens=yes
        ordertaxa=no
        filename=vysl-BT8;

    [ Go! ]
    mcmc;
sump burnin=250;
sumt burnin=250;


end;

Lines at the and (sump and sumt) are mostly necessary for 3.2 version, because they summarize the results.

Usage with Parallel

If you need to run more MrBayes runs in parallel (for example for more genes separately), one of possibilities is use of Parallel, which is library allowing user to launch more parallel processes on more CPU cores or computers. Basic use can look like this:

module add parallel
module add mrbayes/3.2.2

ls *.nexus | parallel -j 10 'echo Start > {}.log && date >> {}.log && mb {} | tee -a {}.log && echo End: >> {}.log && date >> {}.log'

Parameter -j 10 says to use 10 CPU cores. See manual of the function. Remaining commands produce nice logs with time stamps.

Example:

ls *.nexus | parallel -j 10 'mb {}'