You can start by following the tutorials available on the MrBayes manual: http://mrbayes.sourceforge.net/mb3.2_manual.pdf

Dear Animesh Sen

First, You should CONVERT the MAS file to a nexus file and save it in the same folder as the MrBayes.

RECOMMENDATION:

-Place the outgroup taxon in the first rank

-CHOOSE A SHORT FILE NAME

Second, open the file and copy the commands at the end of the sequences that run GTR+G+I model for a nuclear data set. You should modify some commands based on your data (I put them in [...])

Note: There are many details. So read the manual carefully to learn how to change the commands. Since you want to analyze a ribosomal marker, choosing a suitable DNA model (command nucmodel) is crucial.

begin mrbayes;

log start filename= [same as nexus file's name].log;

outgroup 1;

set autoclose=yes nowarn=no;

lset coding=all nucmodel= 4by4 nst=6 rates=invgamma ngammacat=4;

prset Revmatpr=dirichlet(1,1,1,1,1,1) statefreqpr=dirichlet(10,10,10,10) shapepr=exponential (0.05) pinvarpr=uniform(0,1) topologypr=uniform Brlenspr=unconstrained:exp(100.0) ratepr=variable;

mcmcp filename=[PREFERRED NAME] nchains=4 nruns=2 samplefreq=100 printfreq=1000 savebrlens=yes mcmcdiagn=yes diagnfreq=1000 stoprule=YES stopval=0.01 minpartfreq=0.05 relburnin=yes burninfrac=.25;

mcmc;

sump burninfrac=.25;

sumt burninfrac=.25;

log stop;

end;

Third: open Mrbayes and write:

exe [FILE NAME].nex

Now you can have a coffee!

Thank you very much.