MrBayes Block Form - The Santos Lab

A simple form to generate a block for John Huelsenbeck and Fredrik Ronquist's phylogenetic program MrBayes. Simply fill in the values you want, click on the button, and paste the result at the end of your NEXUS data file. Remember if data is interleaved, set interleave=yes in data file).

Form created by Rod Page

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Base file name for results:

Likelihood model (lset)

number of substitution types (nst)
rate variation across sites (rates)
site partition (sitepartition)	(only relevant if site specific model chosen)
base frequencies (basefreq)
molecular clock (clock)

Markov chain Monte Carlo parameters (mcmcp)

number of generations (ngen)	(1000 for a trial, 500,000 + for real)
sample a tree every	generations (samplefreq)
print to screen every	generations (printfreq)
number of chains (nchains)
save tree branch lengths (savebrlens)

Summarise results (sumt)

discard first	trees sampled (burnin) (100 for test, 1000 for real)
consensus tree type (contype)