title: Approaching Long Genomic Regions and Large Recombination Rates with msParSm as an Alternative to MaCS.
abstract: The msParSm application is an evolution of msPar, the parallel version of the coalescent simulation program ms, which removes the limitation for simulating long stretches of DNA sequences with large recombination rates, without compromising the accuracy of the standard coalescence. This work introduces msParSm, describes its significant performance improvements over msPar and its shared memory parallelization details, and shows how it can get better, if not similar, execution times than MaCS. Two case studies with different mutation rates were analyzed, one approximating the human average and the other approximating theDrosophila melanogasteraverage. Source code is available at https://github.com/cmontemuino/msparsm.
authors.affiliation: Computer Architecture and Operating Systems Department (CAOS), Universitat Autònoma de Barcelona, Bellaterra, Spain.
authors.forename: Carlos
authors.initials: C
authors.lastname: Montemuiño
authors.affiliation: Computer Architecture and Operating Systems Department (CAOS), Universitat Autònoma de Barcelona, Bellaterra, Spain.
authors.forename: Antonio
authors.initials: A
authors.lastname: Espinosa
authors.affiliation: Computer Architecture and Operating Systems Department (CAOS), Universitat Autònoma de Barcelona, Bellaterra, Spain.
authors.forename: Juan C
authors.initials: JC
authors.lastname: Moure
authors.affiliation: Centre for Research in Agricultural Genomics (CRAG) Consortium CSIC-IRTA-UAB-UB Edifici CRAG, Campus UAB, Bellaterra, Spain.
authors.forename: Gonzalo
authors.initials: G
authors.lastname: Vera
authors.affiliation: Computer Architecture and Operating Systems Department (CAOS), Universitat Autònoma de Barcelona, Bellaterra, Spain.
authors.forename: Porfidio
authors.initials: P
authors.lastname: Hernández
authors.affiliation: Centre for Research in Agricultural Genomics (CRAG) Consortium CSIC-IRTA-UAB-UB Edifici CRAG, Campus UAB, Bellaterra, Spain.
authors.forename: Sebastián
authors.initials: S
authors.lastname: Ramos-Onsins
keywords: HPC; MPI; coalescence; recombination; sequential Markov coalescent