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# MrBayes (custom)

- DESCRIPTION
- PARAMETERS
- LICENSE

## DESCRIPTION

### 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.

### http://mrbayes.sourceforge.net/manual.php

## 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;
        sump;
        sumt Outputname=mrbayes_out Conformat=simple;
    end;

NOTES
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.

## LICENSE

### GNU GENERAL PUBLIC LICENSE Version 2, June 1991