MrBayes: Bayesian Inference of Phylogeny

Manual and Other Resources

Manual

A good resource for new users is the MrBayes 3.1 manual, which contains instructions for downloading and installing the program, two tutorials including a qick-start version, discussions of all the models implemented in the program, answers to some frequently asked questions, a list of the differences between versions 2 and 3 of the program, instructions for compiling and running the parallel version of the program, and tips for users who want to tweak the source code or contribute bug fixes or new functionality. 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.

Wiki Manual

We are in the process of moving over the information in the current manual to the MrBayes Wiki site. Like the Wikipedia, the content of the Wiki Manual to MrBayes can be edited by all users. This provides an easy mechanism by which users can correct minor mistakes in the manual. Experienced users can also provide tips to beginners and developers can describe details in the algorithmic implementations of various features. There will be a section for Frequently Asked Questions where users can type in questions and other users or the authors of the program can contribute answers. We also plan to have a page for requests of new features.

To contribute to the Wiki, you need to register first. The registration procedure is simple: you select a user name and password and then identify yourself with an email address. According to Wiki conventions, your user name should be in the format Firstname.Lastname, as in 'Mary.Smith'.

If the Wiki site works well, we plan to use it as the main version of the manual for MrBayes 3 as well as for future releases of the program.

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 ' 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. If you prefer not to produce this file yourself, you can download a pdf copy here

HTML help

E-mail List

Finally, a good resource for resolving problems with MrBayes is the MrBayes mailing list. You can ask a question about MrBayes by simply posting a message to this list. Before you can send a message to the list, however, you need to subscribe to it as explained on the home page of the mailing list (see the link above). The list archive is accessible to everyone.

General Advice

Remember that MrBayes is free software and that the authors need to prioritize the development of the program over help to individual users. MrBayes currently has thousands of users around the world and there is no possibility for the authors 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 this does not help, use either the MrBayes email list or the FAQ on the MrBayes Wiki site to pose your question. If the problem you are having seems to be a bug in the program, report it using the bug reporting tool provided on SourceForge, as described here. If you have general questions about the MrBayes project, the models and MCMC sampling algorithms implemented in the program, or the future development of the project, you are welcome to email the authors directly.