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.

Please join the Bayallele-users mailing list here. Release information will be posted via the mailing list. Please feel free to pose any questions you may have regarding this project or the application.

[4th March 2005] New screenshots now available. Click here

Learn more

Population Genetics
Population Genetics Made Simple - Nice primer to the principles of population genetics.
The Estimation of Genetic Distance and Population Substructure from Microsatellite allele frequency data. - Title of paper is self explanatory.
Genepop - Population genetics software.
STR DNA Internet Database - More than you ever wanted to know about microsatellites.
Software for Population Genetic Analysis - Webpage at LSU with links to additional population genetics software.
BATWING - BATWING is a program written in C for the analysis of population genetic data, written by Ian Wilson, now at the University of Aberdeen. Download it here.
Markov Chain Monte Carlo
MCMC Preprint Service - Enough MCMC documentation to keep you occupied for several generations.
MCMC Tutorial - A tutorial in MCMC at the Faculty of Mathematical Studies, University of Southampton.
Bayesian Inference
An Introduction To Parameter Estimation Using Bayesian Probability Theory - Approachable Bayesian Theory paper.
Copyright © 2003, Bayallele Project