Frequently Asked Questions

1: Application

1.1: What is Bayallele?

Bayallele is a Java-based application that uses Bayesian inference and markov chain monte carlo methods to analyse genetic data. The original application upon which Bayallele is based can be found here.

1.2: Why are you developing Bayallele?

Initially, Bayallele is being developed as part of the course requirements for the Bioinformatics degree being pursued by the the three undergraduates whom are developing the application. The main motivation for the development of the application though is to provide interested individuals with a user friendly application/tool that will enable them to carry out data analysis similar to those described in the original scientific paper authored by Nichols and Freeman.

1.3: Is Bayallele Open Source and if so, can I contribute to the project?

Yes...and no. The intention is to release the code as soon as it has been assessed as part of the requirements for the Bioinformatics degree programme at QMUL. We hope to have a final "gold" release ready for April 2004 but will have point releases between now and when the final version is ready. We will gladly accept contribution in the form of bug-finding in the meantime ;-). If you are interested in helping us out this way, please subscribe to the mailing list in the first instance. Unfortunately, until the final version is ready and has been assessed, we are unable to accept code contributions.

1.4: What platform / OS do you support?

Bayallele is Java-based, so we will be able to run on any platform with a JRE version greater than 1.4.

1.5: You say that Bayallele is going to be Open Source, what license are you using?

We plan to release Bayallele under the GNU GPL.

1.6: Where does Genepop fit in?

The application is designed to take its input in the Genepop file format. We hope to be able to support both the two-digit and three-digit allele representation formats. Longer term, we intend to move to an XML file format.