Population Genetic Inference From Resequencing Data

This article is concerned with statistical modeling of shotgun resequencing data and the use Of Such data for population genetic inference. We model data produced by sequencing-by-synthesis technologies such as the Solexa, 454, and polymerase colony (polony) systems, whose Use is becoming increasingly widespread. We show how Such data can be used to estimate evolutionarily parameters (Mutation and recombination rates), despite the fact that the data do not necessarily provide complete or aligned sequence information. We also present two refinements of our methods: one that, is more robust. to sequencing errors and another that. call be used when no reference genome is available.