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MrBayes 3.1 Manual

Fredrik Ronquist, John P. Huelsenbeck and Paul van der Mark

Contents

This manual is still work in progress.

1. Introduction
   1. Conventions Used in this Manual
   2. Acquiring and Installing MrBayes
   3. Getting Started
   4. Changing the Size of the MrBayes Window
   5. Getting Help
   6. Reporting and Fixing Bugs
   7. License and Warranty
2. Tutorial: A Simple Analysis
   1. Quick Start Version
   2. Getting Data into MrBayes
   3. Specifying a Model
   4. Setting the Priors
   5. Checking the Model
   6. Setting up the Analysis
   7. Running the Analysis
   8. When to Stop the Analysis
   9. Summarizing Samples of Substitution Model Parameters
   10. Summarizing Samples of Trees and Branch Lengths
3. Analyzing a Partitioned Data Set
   1. Getting Mixed Data into MrBayes
   2. Dividing the Data into Partitions
   3. Specifying a Partitioned Model
   4. Running the Analysis
4. Evolutionary Models Implemented in MrBayes 3
   1. Nucleotide Models
      1. Simple Nucleotide Models
      2. The Doublet Model
      3. Codon Models
   2. Amino-acid Models
      1. Fixed Rate Models
      2. Estimating the Fixed Rate Model
      3. Variable Rate Models
   3. Restriction Site (Binary) Model
   4. Standard Discrete (Morphology) Model
   5. Parsimony Model
   6. Rate Variation Across Sites
      1. Gamma-distributed Rate Model
      2. Autocorrelated Gamma Model
      3. Proportion of Invariant Sites
      4. Partitioned (Site Specific) Rate Model
      5. Inferring Site Rates
   7. Rate Variation Across the Tree: The Covarion Model
   8. Topology and Branch Length Models
      1. Unconstrained and Constrained Topology
      2. Non-clock (Standard) Trees
      3. Strict Clock Trees
      4. Relaxed Clock Trees
   9. Partitioned Models
   10. Ancestral State Reconstruction
5. Frequently Asked Questions
6. Differences Between Version 2 and Version 3
7. Advanced Topics
   1. Compiling MrBayes
      1. Compiling with GNU Make
      2. Compiling with Code Warrior or Visual Studio
   2. Compiling and Running the Parallel Version of MrBayes
   3. Working with the Source Code
8. Acknowledgements
9. References
10. Appendix: Evolutionary models and proposals in MrBayes