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A Bayesian Model-comparison Approach to Inferring Positive Selection (MBE 2005)

Material for "A Bayesian model-comparison approach to inferring positive selection": Example MrBayes input file: HIV1env.nex is a nexus data file for MrBayes containing aligned sequences from the env gene of HIV-1, along with a MrBayes block setting up the M2 (positive selection) model with F3x4 empirical frequency estimates. I used MrBayes 3.0, of which the distributed version contains bugs in the codon models. I understand that these have been fixed in version 3.1, but haven't tested this. Also the F3x4 empirical frequency estimates had not been implemented last time I checked. Bug-free MrBayes 3.0 source code implementing this is available from me on request. Script for calculating Savage-Dickey ratio: Savage-Dickey.pl is a perl script that will process a .p output file from MrBayes to calculate the Savage-Dickey ratio and associated quantities. - Konrad Scheffler