BPrimm (Bayesian and Penalized regression in multiple loci mapping) includes a set of tools for simultaneously multiple loci mapping, and two novel methods named the Bayesian adaptive Lasso and the Iterative Adaptive Lasso
PSTk-Classifier is a software written in C++ for classifying DNA using a Bayesian approach. Different underlying models can be selected — Naive (Nk), Markov (Mk) and Variable Length Markov (VLMK). The classifier works by first constructing profiles for all groups using fasta-files directly. The profiles are kept in a directory. Then sample sequences (in a multifasta file) can be scored against the profiles and a high-score list will be presented.
BIMBAM (Bayesian IMputation-Based Association Mapping)implements methods for assocation mapping. BIMBAM can handle both large association studies (e.g., genome scans) and smaller studies of candidate genes/regions.
GControl is a computer program for Bayesian analysis of case-control data that controls for population stratification and cryptic relatedness. GControl performs these analyses using Markov chain Monte Carlo algorithms.
HaMMLET is a fast Forward-Backward Gibbs sampler for Bayesian inference on Hidden Markov Models (HMM). It uses the Haar wavelet transform to dynamically compress the data based on the current variance sample in each iteration.
LAMARC (Likelihood Analysis with Metropolis Algorithm using Random Coalescence) is a program which estimates population-genetic parameters such as population size, population growth rate, recombination rate, and migration rates. It approximates a summation over all possible genealogies that could explain the observed sample, which may be sequence, SNP, microsatellite, or electrophoretic data.