Bayesian Inference Presentations

1. Gothenburg Workshop, Dec 2008, presentation I (Bayesian Phylogenetic Inference, MCMC) (PowerPoint presentation).
2. Gothenburg Workshop, Dec 2008, presentation II (MrBayes) (PowerPoint presentation).
3. Gothenburg Workshop, Dec 2008, presentation III (Unusual Character Types: Restriction Sites, Morphology, Bayesian Model Choice) (PowerPoint presentation).
4. Gothenburg Workshop, Dec 2008, Woods Hole, August 2005 (Biogeography Model, Complex Models, Critiques of Bayesian Phylogenetic Inference) (PowerPoint presentation).
5. Molecular Evolution Workshop, July 2009 (Bayesian Phylogenetic Inference) (Powerpoint presentation).
6. Molecular Evolution Workshop, January 2010 (MrBayes intro) (Powerpoint presentation).

MrBayes Resources

1. MrBayes web site.
2. MrBayes version 3.1 manual (pdf) containing two tutorials that will introduce you to the program
3. MrBayes version 3.1 online html help
4. MrBayes versions 3.1 and 3.2 Wiki manual
5. MrBayes version 3.2 manual (pdf) containing updated tutorials
6. Cheat sheet (pdf) describing how to download and compile MrBayes 3.2 from source code in regular or MPI version.
7. Additional MrBayes 3.2 tutorials covering some more advanced features of the program (word document (pdf))

Books and Papers on MrBayes and Bayesian Phylogenetic Inference

1. MrBayes chapter (pdf) (version 3.1) in "Statistical Methods in Molecular Evolution" (Nielsen ed.).
2. MrBayes chapter (pdf) (version 3.2) in "The Phylogenetic Handbook" (Lemey et al., eds).
3. Review of Bayesian phylogenetics in Annual Review of Entomology (2010).

Data Sets

Data sets for the tutorials mentioned above and for particular types of models or analyses:
1. First tutorial in the manual (and "The Phylogenetic Handbook"): primates.nex
2. Second tutorial in the manual (and "The Phylogenetic Handbook"): cynmix.nex
3. Tutorial in "Statistical Methods in Molecular Evolution": kim.nex
4. Data set with instructions for codon and positive selection models: codon.nex
5. Example data set for calibrated (dated) analysis with tip and node caliraibrations under cpp relaxed clock model: hymfossil.nex
6. Toy example showing how to set up the BEST model: best_test.nex

Intro to R for Phylogenetics and MrBayes Output Analysis

1. Intro to R for phylogenetics: BasicIntroduction_R_for_Phylogenetics.r
2. Tree for previous script: sampleTree.nwk
3. Data for tree in previous script: data_for_tree.txt
4. Example script for reading and plotting MrBayes output: RScript_SummarizeMrBayesFiles.r