How do I run MrBayes in batch mode?
When you become more familiar with MrBayes, you will undoubtedly want to run it in batch mode instead of typing all commands at the prompt. This is done by adding a MRBAYES block to a Nexus file, either the same file containing the DATA block or a separate Nexus file. The MRBAYES block simply contains the commands as you would have given them from the command line, with the difference that each command line is ended with a semi-colon. For instance, a MRBAYES block that performs three single-run analyses of the data setprimates.nex under the GTR + Γ model and stores each result in a separate file is given below: begin mrbayes; set autoclose=yes nowarn=yes; execute primates.nex; lset nst=6 rates=gamma; mcmc nruns=1 ngen=10000 samplefreq=10 file=primates.nex1; mcmc file=primates.nex2; mcmc file=primates.nex3; end; Since this file contains the “execute” command, it must be in a file separate from the primates.nex file. You start the analysis simply by typing execute
