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

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 introdu...

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Autores: Montemuiño Sosa, Carlos, Espinosa, Antonio|||0000-0002-6460-3789, Moure, Juan C.|||0000-0001-6697-0331, Vera Rodríguez, Gonzalo|||0000-0001-6990-0216, Hernández Budé, Porfidio|||0000-0002-8592-934X, Ramos Onsins, Sebastián Ernesto|||0000-0002-1776-140X
Tipo de recurso: artículo
Fecha de publicación:2016
País:España
Institución:Universitat Autònoma de Barcelona
Repositorio:Dipòsit Digital de Documents de la UAB
Idioma:inglés
OAI Identifier:oai:ddd.uab.cat:186001
Acceso en línea:https://ddd.uab.cat/record/186001
https://dx.doi.org/urn:doi:10.4137/EBO.S40268
Access Level:acceso abierto
Palabra clave:Coalescence
Recombination
Sequential Markov coalescent
HPC
MPI
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spelling Approaching long genomic regions and large recombination rates with msParSm as an alternative to MaCSMontemuiño Sosa, CarlosEspinosa, Antonio|||0000-0002-6460-3789Moure, Juan C.|||0000-0001-6697-0331Vera Rodríguez, Gonzalo|||0000-0001-6990-0216Hernández Budé, Porfidio|||0000-0002-8592-934XRamos Onsins, Sebastián Ernesto|||0000-0002-1776-140XCoalescenceRecombinationSequential Markov coalescentHPCMPIThe 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. 22016-01-0120162016-01-01Articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://ddd.uab.cat/record/186001https://dx.doi.org/urn:doi:10.4137/EBO.S40268reponame:Dipòsit Digital de Documents de la UABinstname:Universitat Autònoma de BarcelonaInglésengMinisterio de Economía y Competitividad https://doi.org/10.13039/501100003329 TIN2014-53234-C2-1-RMinisterio de Economía y Competitividad https://doi.org/10.13039/501100003329 AGL2013-41834-Ropen accesshttp://purl.org/coar/access_right/c_abf2Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, sempre que no sigui amb finalitats comercials, i sempre que es reconegui l'autoria de l'obra original.https://creativecommons.org/licenses/by-nc/3.0/info:eu-repo/semantics/openAccessoai:ddd.uab.cat:1860012026-06-06T12:50:31Z
dc.title.none.fl_str_mv Approaching long genomic regions and large recombination rates with msParSm as an alternative to MaCS
title Approaching long genomic regions and large recombination rates with msParSm as an alternative to MaCS
spellingShingle Approaching long genomic regions and large recombination rates with msParSm as an alternative to MaCS
Montemuiño Sosa, Carlos
Coalescence
Recombination
Sequential Markov coalescent
HPC
MPI
title_short Approaching long genomic regions and large recombination rates with msParSm as an alternative to MaCS
title_full Approaching long genomic regions and large recombination rates with msParSm as an alternative to MaCS
title_fullStr Approaching long genomic regions and large recombination rates with msParSm as an alternative to MaCS
title_full_unstemmed Approaching long genomic regions and large recombination rates with msParSm as an alternative to MaCS
title_sort Approaching long genomic regions and large recombination rates with msParSm as an alternative to MaCS
dc.creator.none.fl_str_mv Montemuiño Sosa, Carlos
Espinosa, Antonio|||0000-0002-6460-3789
Moure, Juan C.|||0000-0001-6697-0331
Vera Rodríguez, Gonzalo|||0000-0001-6990-0216
Hernández Budé, Porfidio|||0000-0002-8592-934X
Ramos Onsins, Sebastián Ernesto|||0000-0002-1776-140X
author Montemuiño Sosa, Carlos
author_facet Montemuiño Sosa, Carlos
Espinosa, Antonio|||0000-0002-6460-3789
Moure, Juan C.|||0000-0001-6697-0331
Vera Rodríguez, Gonzalo|||0000-0001-6990-0216
Hernández Budé, Porfidio|||0000-0002-8592-934X
Ramos Onsins, Sebastián Ernesto|||0000-0002-1776-140X
author_role author
author2 Espinosa, Antonio|||0000-0002-6460-3789
Moure, Juan C.|||0000-0001-6697-0331
Vera Rodríguez, Gonzalo|||0000-0001-6990-0216
Hernández Budé, Porfidio|||0000-0002-8592-934X
Ramos Onsins, Sebastián Ernesto|||0000-0002-1776-140X
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Coalescence
Recombination
Sequential Markov coalescent
HPC
MPI
topic Coalescence
Recombination
Sequential Markov coalescent
HPC
MPI
description 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.
publishDate 2016
dc.date.none.fl_str_mv 2
2016-01-01
2016
2016-01-01
dc.type.none.fl_str_mv Article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://ddd.uab.cat/record/186001
https://dx.doi.org/urn:doi:10.4137/EBO.S40268
url https://ddd.uab.cat/record/186001
https://dx.doi.org/urn:doi:10.4137/EBO.S40268
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.relation.none.fl_str_mv Ministerio de Economía y Competitividad https://doi.org/10.13039/501100003329 TIN2014-53234-C2-1-R
Ministerio de Economía y Competitividad https://doi.org/10.13039/501100003329 AGL2013-41834-R
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
https://creativecommons.org/licenses/by-nc/3.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
https://creativecommons.org/licenses/by-nc/3.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:Dipòsit Digital de Documents de la UAB
instname:Universitat Autònoma de Barcelona
instname_str Universitat Autònoma de Barcelona
reponame_str Dipòsit Digital de Documents de la UAB
collection Dipòsit Digital de Documents de la UAB
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