A Markov chain Monte Carlo sampler for gene genealogies conditional on haplotype data

The gene genealogy is a tree describing the ancestral relationships among genes sampled from unrelated individuals. Knowledge of the tree is useful for inference of population-genetic parameters such as migration or recombination rates. It also has potential application in gene-mapping, as individuals with similar trait values will tend to be more closely related genetically at the location of a trait-inuencing mutation. One way to incorporate genealogical trees in genetic applications is to sample them conditional on observed genetic data. We have implemented a Markov chain Monte Carlo based genealogy sampler that conditions on observed haplotype data. Our implementation is based on