Manual and Other Resources
Manual
A good resource for new users is the MrBayes 3.2 manual, which contains instructions for downloading and installing the program, two tutorials including a quick-start version, discussions of all the models implemented in the program, answers to some frequently asked questions, and a list of the differences between versions 2 and 3 of the program. In an appendix, there is a diagrammatic summary of all the models implemented in the program and most of the proposal mechanisms. You can download the manual (pdf) here.
Online Help
MrBayes 3 provides extensive online help through the help command. Simply type help at the command prompt to get a list of the available commands. Type help <command> to get help information for a specific command. For instance, help lset will give you the help information for the lset command, including a discussion of all the available parameters and options. The help information for a command typically also includes a summary table of the options and current settings.
Command Reference
You can produce a text file containing all the help information for the current version of the program by using the manual command in MrBayes. If you produce this file immediately after starting the program, the text file will contain all the default settings and can be used as a command reference.
General Advice
Remember that MrBayes is free software and that it currently has thousands of users around the world. Therefore, the authors have no possibility to provide extensive user help. Please first read the manual and the command reference carefully to make sure the problem you are having is not addressed there. If the problem you are having seems to be a bug in the program, report it as described here.
Citing MrBayes
If you publish results obtained using MrBayes you may want to cite the program using one of these papers:
- Huelsenbeck, J.P., and F. Ronquist. 2001. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17:754-755.
- Ronquist, F., and J.P. Huelsenbeck. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
- Ronquist, F., M. Teslenko, P. van der Mark, D.L. Ayres, A. Darling, S. Höhna, B. Larget, L. Liu, M.A. Suchard, and J.P. Huelsenbeck. 2012. MRBAYES 3.2: Efficient Bayesian phylogenetic inference and model selection across a large model space. Syst. Biol. 61:539-542.
If you use the parallel abilities of the program, you may also want to cite:
- Altekar, G., S. Dwarkadas, J. P. Huelsenbeck, and F. Ronquist. 2004. Parallel Metropolis-coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 20:407-415.
If you use the BEAGLE library, the appropriate citation is:
- Ayres, D.L., A. Darling, D.J. Zwickl, P. Beerli, M.T. Holder, P.O. Lewis, J.P. Huelsenbeck, F. Ronquist, D. L. Swofford, M. P. Cummings, A. Rambaut, and M. A. Suchard. 2012. BEAGLE: an application programming interface for statistical phylogenetics. Syst. Biol. 61:170-173.
You may also see further citations for substitution models, computational methods implemented, etc, by issuing the citations command in MrBayes.