Approaching Long Genomic Regions and Large Recombination Rates with msParSm as an Alternative to MaCS

Carlos Montemuiño, Antonio Espinosa, Juan C. Moure, Gonzalo Vera, Porfidio Hernández, Sebastián Ramos-Onsins
2016 Evolutionary Bioinformatics  
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.
more » ... o 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.
doi:10.4137/ebo.s40268 pmid:27721650 pmcid:PMC5047705 fatcat:2j2bbo5einhbrcpnhg3au7zxpi