Approaching long genomic regions and large recombination rates with msParSm as an alternative to MaCS

Carlos Montemuiño; Antonio Espinosa; Gonzalo Vera; Porfidio Hernández; Sebastián Ramos-Onsins; Juan Carlos Moure Lopez

doi:https://doi.org/10.4137/EBO.S40268

Approaching long genomic regions and large recombination rates with msParSm as an alternative to MaCS

Carlos Montemuiño, Antonio Espinosa, Gonzalo Vera, Porfidio Hernández, Sebastián Ramos-Onsins, Juan Carlos Moure Lopez

Research output: Contribution to journal › Article › Research › peer-review

Abstract

© 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.

Original language	English
Pages (from-to)	223-228
Journal	Evolutionary Bioinformatics
Volume	12
DOIs	https://doi.org/10.4137/EBO.S40268
Publication status	Published - 2 Oct 2016

Keywords

Coalescence
HPC
MPI
Recombination
Sequential Markov coalescent

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https://ddd.uab.cat/record/186001

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title = "Approaching long genomic regions and large recombination rates with msParSm as an alternative to MaCS",

abstract = "{\textcopyright} 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.",

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year = "2016",

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language = "English",

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Approaching long genomic regions and large recombination rates with msParSm as an alternative to MaCS. / Montemuiño, Carlos; Espinosa, Antonio; Vera, Gonzalo; Hernández, Porfidio; Ramos-Onsins, Sebastián; Moure Lopez, Juan Carlos.

In: Evolutionary Bioinformatics, Vol. 12, 02.10.2016, p. 223-228.

Research output: Contribution to journal › Article › Research › peer-review

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AU - Montemuiño, Carlos

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AU - Vera, Gonzalo

AU - Hernández, Porfidio

AU - Ramos-Onsins, Sebastián

AU - Moure Lopez, Juan Carlos

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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

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