title: IMa2p--parallel MCMC and inference of ancient demography under the Isolation with migration (IM) model.
abstract: IMa2 and related programs are used to study the divergence of closely related species and of populations within species. These methods are based on the sampling of genealogies using MCMC, and they can proceed quite slowly for larger data sets. We describe a parallel implementation, called IMa2p, that provides a nearly linear increase in genealogy sampling rate with the number of processors in use. IMa2p is written in OpenMPI and C++, and scales well for demographic analyses of a large number of loci and populations, which are difficult to study using the serial version of the program.
authors.affiliation: Center for Computational Genetics and Genomics, Department of Biology, Temple University, Philadelphia, PA, 19102, USA.
authors.forename: Arun
authors.initials: A
authors.lastname: Sethuraman
authors.affiliation: Center for Computational Genetics and Genomics, Department of Biology, Temple University, Philadelphia, PA, 19102, USA.
authors.forename: Jody
authors.initials: J
authors.lastname: Hey
mesh_terms: D000465:Algorithms; D003710:Demography; D051456:Gene Flow; D008390:Markov Chains; D008957:Models, Genetic; D009010:Monte Carlo Method; D059645:Mutation Rate; D012984:Software
keywords: Isolation with migration; MCMC; Metropolis coupling; Parallelization; message passing interface