MrBayes + PAUP + MrModeltest on Windows

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.


Input files

  • Your multiple sequence alignment file in NEXUS format.


Download the package (MrBayes + PAUP + MrModeltest) here and extract all files in your directory. After this, paste your NEXUS file in the same directory of MrBayes package downloaded.

Open Paup in PAUP.exe

In PAUP.exe execute:

  • exec your_alignment.nex
    wait for complete message
  • exec mrmodelblock.nex
    this process may take few minutes. Wait for message: “Processing of file “mrmodelblock.nex” completed.

close PAUP.exe

Open PROMPT file and execute:

  • mrmodeltest.exe < mrmodel.scores > out.txt
    here you created the file out.txt that contains the best nucleotide substitution model that fit in your data.

close PROMPT.

Open the file out.txt and copy (ctrl + C) the info between the lines “BEGIN MRBAYES;” and “END;”:


Lset nst=6 rates=invgamma;
Prset statefreqpr=dirichlet(1,1,1,1);

Open your alignment (NEXUS file). Paste (ctrl + V) the information from out.txt to the end of your alignment file.

Paste the following line before the “END;” line:

  • mcmc ngen=1000000 samplefreq=500 printfreq=5000 diagnfreq=50000;

In this line you are setting 1 million of generations and others parameters to MrBayes software.

close your NEXUS file.

Open MRBAYES.exe and execute:

  • exec your_alignment.nex

No need for more generations if the standard deviation is below 0.01.

Next, execute:

  • sump
    observe distribuions of posterior probability
  • sump burnin=250
    increase value if necessary
  • sumt burnin=250 (same value as in sump)

Close the MRBAYES.exe and find your tree in file *nex.con.

You can open the tree file in Figtree.

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2 Responses to MrBayes + PAUP + MrModeltest on Windows

  1. Adso Mendes says:

    Nice, but I’ve tried to download the package and it’s no longer available.

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