Lab 29 - MrBayes 3.1.2
Biol 615 Systematics and Comparative Biology, (Sikes)
This lab, and many of the subsequent labs, will not be graded. You can complete this lab at your leisure. MRBayes is a free download and you can install it on any Unix, PC, or Mac computer on which you have permission to do so. The program is available here: http://mrbayes.sourceforge.net/index.php
This lab is based, heavily, on labs prepared by two phylo-statisticians who know far more about Bayesian analysis than I do: Paul Lewis and Fredrik Ronquist (these guys really know this stuff - they write the programs - Ronquist is the co-developer of MrBayes).
1. Locate the primates.nex file in the examples folder inside the MrBayes folder
2. Work through the tutorial prepared by F. Ronquist
3. Add a MrBayes block to the datafile
A program for Bayesian inference that can implement a ´mixture model´ (Pagel and Meade, 2004) allowing the user to fit more than one model of sequence evolution, without partitioning the data.
For those interested in Bayesian inference this program is worth investigating. The mixture-model approach is a very powerful method to detect significant partitions in your data.
Pagel, M. and Meade, A. (2004) A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data. Syst Biol 53: 571-581.