Title: Ancestral inference from haplotypes and mutations,
Abstract: We consider inference about the history of a sample of DNA sequences,
conditional upon the haplotype counts and the number of segregating sites
observed at the present time. After deriving some theoretical results in the
coalescent setting, we implement rejection sampling and importance sampling
schemes to perform the inference. The importance sampling scheme addresses an
extension of the Ewens Sampling Formula for a configuration of haplotypes and
the number of segregating sites in the sample. The implementations include both
constant and variable population size models. The methods are illustrated by
two human Y chromosome data sets.