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    MrBayes (custom)


    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.



    MrBayes command file

    This option allows you to provide a custom MrBayes command file. A command file may contain any command that is normally issued inside the MrBayes shell, with the difference that each command line is ended with a semi-colon.
    You can use the following minimal example as a starting point for your own command files.
    begin mrbayes;
        set autoclose=yes nowarn=yes;
        lset nst=6 rates=propinv;
        mcmc ngen=100000;
        sumt Outputname=mrbayes_out Conformat=simple;
    The consensus tree has to be named mrbayes_out. Otherwise ARB will not be able to import it.
    It is not necessary to include any kind of data loading command. The selected sequences will be loaded automatically.


    GNU GENERAL PUBLIC LICENSE Version 2, June 1991