source: branches/profile/GDEHELP/HELP_WRITTEN/MrBayesCustom.help

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1MrBayes (custom)
2
3DESCRIPTION
4        MrBayes is a program for Bayesian inference and model choice across
5        a wide range of phylogenetic and evolutionary models. MrBayes uses
6        Markov chain Monte Carlo (MCMC) methods to estimate the posterior
7        distribution of model parameters.
8
9        http://mrbayes.sourceforge.net/manual.php
10           
11
12PARAMETERS
13     
14    MrBayes command file
15
16        This option allows you to provide a custom MrBayes command file.
17        A command file may contain any command that is normally issued
18        inside the MrBayes shell, with the difference that each command line
19        is ended with a semi-colon.
20       
21        You can use the following minimal example as a starting point for your own
22        command files.
23           
24            begin mrbayes;
25                set autoclose=yes nowarn=yes;
26                lset nst=6 rates=propinv;
27                mcmc ngen=100000;
28                sump;
29                sumt Outputname=mrbayes_out Conformat=simple;
30            end;
31           
32           
33        NOTES
34               
35            The consensus tree has to be named mrbayes_out. Otherwise ARB will not
36            be able to import it.
37           
38            It is not necessary to include any kind of data loading command.
39            The selected sequences will be loaded automatically.
40           
41
42       
43LICENSE
44        GNU GENERAL PUBLIC LICENSE
45        Version 2, June 1991
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