title: Population genetic inference from resequencing data.
abstract: 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 evolutionary 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 can be used when no reference genome is available.
authors.affiliation: Department of Oncology, University of Cambridge, Cambridge CB2 0RE, UK.
authors.forename: Rong
authors.initials: R
authors.lastname: Jiang
authors.forename: Simon
authors.initials: S
authors.lastname: Tavaré
authors.forename: Paul
authors.initials: P
authors.lastname: Marjoram
mesh_terms: D004171:Diploidy; D005828:Genetics, Population; D015894:Genome, Human / Q000235:genetics; D006720:Homozygote; D006801:Humans; D015810:Linkage Disequilibrium / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*