Motivation: The diversity of a haplotype, represented as a string of polymorphic sites along a DNA sequence, increases exponentially with the number of sites if recombinations are taking place. Reconstructing the history of recombinations compared with that of the polymorphic sites is thus extremely difficult. However, in the human genome, because of the relatively simple pattern of haplotype diversity dominated by a few ancestral haplotypes, the complexity of the recombinational network can be reduced, thus making its reconstruction feasible. We focus on the problem of inferring the recombination pathways starting with putative ancestral haplotypes and leading to new rare recombinant haplotypes. Results: We describe classes of recombinations that represent the whole set of minimal recombination pathways leading to a new haplotype. We present an O(n2) algorithm that outputs such representative recombination pathways. We apply it to haplotypes of the 8 kb dystrophin gene segment dys44.
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