A Hybrid Parallel Neighbor-Joining Algorithm for Phylogenetic Tree Reconstruction on a Multicore Cluster

Autores
Rucci, Enzo; Chichizola, Franco; Naiouf, Marcelo; De Giusti, Armando Eduardo
Año de publicación
2013
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Building phylogenetic trees is one of the significant applications within bioinformatics, mainly due to its involvement in multiple sequence alignment. Because of the high computational complexity required, the use of parallel processing during the building process is convenient. Taking into account that current cluster architectures are hybrid, in this paper we present a parallel algorithm to build phylogenetic trees based on the Neighbor-Joining method, which uses a hybrid communication model (combination of message passing and shared memory), and then analyze its performance. Finally, conclusions and possible future lines of work are presented
Facultad de Informática
Materia
Ciencias Informáticas
Parallel programming languages
Hybrid Programming
Multicore Cluster
Phylogenetic Trees
Neighbor-Joining Method
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by-nc/4.0/
Repositorio
SEDICI (UNLP)
Institución
Universidad Nacional de La Plata
OAI Identificador
oai:sedici.unlp.edu.ar:10915/80066
Acceder
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oai_identifier_str oai:sedici.unlp.edu.ar:10915/80066
network_acronym_str SEDICI
repository_id_str 1329
network_name_str SEDICI (UNLP)
spelling A Hybrid Parallel Neighbor-Joining Algorithm for Phylogenetic Tree Reconstruction on a Multicore ClusterRucci, EnzoChichizola, FrancoNaiouf, MarceloDe Giusti, Armando EduardoCiencias InformáticasParallel programming languagesHybrid ProgrammingMulticore ClusterPhylogenetic TreesNeighbor-Joining MethodBuilding phylogenetic trees is one of the significant applications within bioinformatics, mainly due to its involvement in multiple sequence alignment. Because of the high computational complexity required, the use of parallel processing during the building process is convenient. Taking into account that current cluster architectures are hybrid, in this paper we present a parallel algorithm to build phylogenetic trees based on the Neighbor-Joining method, which uses a hybrid communication model (combination of message passing and shared memory), and then analyze its performance. Finally, conclusions and possible future lines of work are presentedFacultad de Informática2013-03-15info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionArticulohttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdf74-80http://sedici.unlp.edu.ar/handle/10915/80066enginfo:eu-repo/semantics/altIdentifier/issn/2304-9464info:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc/4.0/Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)reponame:SEDICI (UNLP)instname:Universidad Nacional de La Platainstacron:UNLP2025-09-03T10:46:56Zoai:sedici.unlp.edu.ar:10915/80066Institucionalhttp://sedici.unlp.edu.ar/Universidad públicaNo correspondehttp://sedici.unlp.edu.ar/oai/snrdalira@sedici.unlp.edu.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:13292025-09-03 10:46:56.596SEDICI (UNLP) - Universidad Nacional de La Platafalse
dc.title.none.fl_str_mv A Hybrid Parallel Neighbor-Joining Algorithm for Phylogenetic Tree Reconstruction on a Multicore Cluster
title A Hybrid Parallel Neighbor-Joining Algorithm for Phylogenetic Tree Reconstruction on a Multicore Cluster
spellingShingle A Hybrid Parallel Neighbor-Joining Algorithm for Phylogenetic Tree Reconstruction on a Multicore Cluster
Rucci, Enzo
Ciencias Informáticas
Parallel programming languages
Hybrid Programming
Multicore Cluster
Phylogenetic Trees
Neighbor-Joining Method
title_short A Hybrid Parallel Neighbor-Joining Algorithm for Phylogenetic Tree Reconstruction on a Multicore Cluster
title_full A Hybrid Parallel Neighbor-Joining Algorithm for Phylogenetic Tree Reconstruction on a Multicore Cluster
title_fullStr A Hybrid Parallel Neighbor-Joining Algorithm for Phylogenetic Tree Reconstruction on a Multicore Cluster
title_full_unstemmed A Hybrid Parallel Neighbor-Joining Algorithm for Phylogenetic Tree Reconstruction on a Multicore Cluster
title_sort A Hybrid Parallel Neighbor-Joining Algorithm for Phylogenetic Tree Reconstruction on a Multicore Cluster
dc.creator.none.fl_str_mv Rucci, Enzo
Chichizola, Franco
Naiouf, Marcelo
De Giusti, Armando Eduardo
author Rucci, Enzo
author_facet Rucci, Enzo
Chichizola, Franco
Naiouf, Marcelo
De Giusti, Armando Eduardo
author_role author
author2 Chichizola, Franco
Naiouf, Marcelo
De Giusti, Armando Eduardo
author2_role author
author
author
dc.subject.none.fl_str_mv Ciencias Informáticas
Parallel programming languages
Hybrid Programming
Multicore Cluster
Phylogenetic Trees
Neighbor-Joining Method
topic Ciencias Informáticas
Parallel programming languages
Hybrid Programming
Multicore Cluster
Phylogenetic Trees
Neighbor-Joining Method
dc.description.none.fl_txt_mv Building phylogenetic trees is one of the significant applications within bioinformatics, mainly due to its involvement in multiple sequence alignment. Because of the high computational complexity required, the use of parallel processing during the building process is convenient. Taking into account that current cluster architectures are hybrid, in this paper we present a parallel algorithm to build phylogenetic trees based on the Neighbor-Joining method, which uses a hybrid communication model (combination of message passing and shared memory), and then analyze its performance. Finally, conclusions and possible future lines of work are presented
Facultad de Informática
description Building phylogenetic trees is one of the significant applications within bioinformatics, mainly due to its involvement in multiple sequence alignment. Because of the high computational complexity required, the use of parallel processing during the building process is convenient. Taking into account that current cluster architectures are hybrid, in this paper we present a parallel algorithm to build phylogenetic trees based on the Neighbor-Joining method, which uses a hybrid communication model (combination of message passing and shared memory), and then analyze its performance. Finally, conclusions and possible future lines of work are presented
publishDate 2013
dc.date.none.fl_str_mv 2013-03-15
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
Articulo
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://sedici.unlp.edu.ar/handle/10915/80066
url http://sedici.unlp.edu.ar/handle/10915/80066
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/issn/2304-9464
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by-nc/4.0/
Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc/4.0/
Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
dc.format.none.fl_str_mv application/pdf
74-80
dc.source.none.fl_str_mv reponame:SEDICI (UNLP)
instname:Universidad Nacional de La Plata
instacron:UNLP
reponame_str SEDICI (UNLP)
collection SEDICI (UNLP)
instname_str Universidad Nacional de La Plata
instacron_str UNLP
institution UNLP
repository.name.fl_str_mv SEDICI (UNLP) - Universidad Nacional de La Plata
repository.mail.fl_str_mv alira@sedici.unlp.edu.ar
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score 13.13397

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