AlphaBayes
AlphaBayes is a software package for carrying out genome wide association studies and genomic selection. It implements several Bayesian models and can simultaneously or separately fit SNPs, fixed effects, polygenic, and genetic group effects.
Linux and windows executables, example files, background publications on the method and a user manual are available for download here. Download
If you are going to use it this program it is best contact John Hickey as the downloadable version here is a temporary version. Another version with greater functionality is ready and currently being tested.