MrBayes MPI 3.1
General information and sample Command blocks.

   Submitting NEXUS files to the CCG Phylocluster


There are two ways to submit MrBayes analyses to the CCG Phylocluster:


  1. 1. You may select the "Simple View", submit your     NEXUS file without a command block and use the     provided pull down menus to select parameters     for your analysis.



  2. 2. You may select the "Expert View" and submit     your NEXUS file with a command block already     written to your file.



Simple Command block for MrBayes with a single
model (GTR+I+Γ). It is recommended that you
estimate a model for your data set with MrModeltest2.

Copy all of the text in the white box below and paste into your NEXUS file after the last "end;" EDIT VALUES TO MATCH YOUR DATA!

Begin mrbayes;
  2. log start filename=FILENAME_log.txt;
  3. set autoclose=yes;
  4. lset nst=6 rates=invgamma;
  5. mcmc ngen=50000000 samplefreq=100 printfreq=100 nchains=4 savebrlens=yes;
  6. sump burnin=12500;
  7. sumt burnin=12500;
  8. log stop;

END;


More complex Command block for MrBayes with Multiple partitions and models. It is recommended that you estimate a model for your data set with MrModeltest2.

Copy all of the text in the white box below and paste into your NEXUS file after the last "end;" EDIT VALUES TO MATCH YOUR DATA!

Begin mrbayes;
  2. log start filename=FILENAME_log.txt;
  3. set autoclose=yes;
  4. charset 1stpos = 1-720\3;
  5. charset 2ndpos = 2-720\3;
  6. charset 3rdpos = 3-720\3;
  7. partition bycodon = 3:1stpos,2ndpos,3rdpos;
  8. unlink shape=(all) pinvar=(all) statefreq=(all) revmat=(all);
  9. lset applyto=(1,3) nst=6 rates=invgamma;
  10. lset applyto=(2) nst=2 rates=gamma;
  11. mcmc ngen=50000000 samplefreq=1000 printfreq=1000 nchains=4 savebrlens=yes;
  12. sump burnin=12500;
  13. sumt burnin=12500;
  14. log stop;

END;


Related Links

MrModeltest2 explained

PAUP info and commands

MrBayes info and commands

Clustal W info

RAxML info and commands

PAUP Sets blocks