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