Hidden Markov Modelling Techniques for Haplotype Analysis

Mikko Koivisto, Teemu Kivioja, Heikki Mannila, Pasi Rastas, Esko Ukkonen

Abstract: A hidden Markov model is introduced for descriptive modelling the mosaic–like structures of haplotypes, due to iterated recombinations within a population. Methods using the minimum description length principle are given for fitting such models to training data. Possible applications of the models are delineated, and some preliminary analysis results on real sets of haplotypes are reported, demonstrating the potential of our methods.