TY - JOUR
T1 - Approaching long genomic regions and large recombination rates with msParSm as an alternative to MaCS
AU - Montemuiño, Carlos
AU - Espinosa, Antonio
AU - Vera, Gonzalo
AU - Hernández, Porfidio
AU - Ramos-Onsins, Sebastián
AU - Moure Lopez, Juan Carlos
PY - 2016/10/2
Y1 - 2016/10/2
N2 - © the authors, publisher and licensee Libertas Academica Limited. 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 the Drosophila melanogaster average. Source code is available at https://github.com/cmontemuino/msparsm.
AB - © the authors, publisher and licensee Libertas Academica Limited. 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 the Drosophila melanogaster average. Source code is available at https://github.com/cmontemuino/msparsm.
KW - Coalescence
KW - HPC
KW - MPI
KW - Recombination
KW - Sequential Markov coalescent
U2 - https://doi.org/10.4137/EBO.S40268
DO - https://doi.org/10.4137/EBO.S40268
M3 - Article
VL - 12
SP - 223
EP - 228
ER -