Hidden Markov Modelling Techniques for Haplotype Analysis (invited lecture for DS 2004) Author: Esko Ukkonen Affiliation: Department of Computer Science, University of Helsinki, Helsinki, Finland 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. This is joint work with Mikko Koivisto, Teemu Kivioja, Heikki Mannila, and Pasi Rastas; A research supported by the Academy of Finland under grant 201560. ©Copyright 2004 Author