At the MrBayes > prompt, type mcmc ngen=20000 samplefreq=100
printfreq=100 diagnfreq=1000. This will ensure that you get at least 200
samples from the posterior probability distribution, and that diagnostics are
calculated every 1,000 generations. For larger data sets you probably want to run
the analysis longer and sample less frequently. The default sample and print
frequency is 500, the default diagnostic frequency is 5,000, and the default run
length is 1,000,000. You can find the predicted remaining time to completion of
the analysis in the last column printed to screen