Bayallele, a play on the words "Bayesian" and "allele", is a Java-based application that uses Bayesian inference and markov chain monte carlo methods to analyse genetic data. For each population (p) the analysis obtains separate estimates of population size (Np) and migration rate (mp) along with the mutation rate at each locus (μl). The user can specify diffuse priors, although the analysis is particularly effective with prior information that certain populations are smaller or more isolated than the others, or that loci differ in mutation rate (e.g. SNPs vs microsatellites). It is intended for Bayallele to be complementary to existing population genetics applications such as Genepop.
The original application upon which Bayallele is based can be found here. It was developed in Pascal by Prof. R.A. Nichols as part of his research into the conservation genetics of endemic skinks on Mauritius.