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

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...

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Autores principales: Rucci, Enzo, Chichizola, Franco, Naiouf, Marcelo, De Giusti, Armando Eduardo
Formato: Articulo
Lenguaje:Inglés
Publicado: 2013
Materias:
Ciencias Informáticas
Parallel programming languages
Hybrid Programming
Multicore Cluster
Phylogenetic Trees
Neighbor-Joining Method
Acceso en línea:http://sedici.unlp.edu.ar/handle/10915/80066
Aporte de:
SEDICI (UNLP) de Universidad Nacional de La Plata
id I19-R120-10915-80066
record_format dspace
institution Universidad Nacional de La Plata
institution_str I-19
repository_str R-120
collection SEDICI (UNLP)
language Inglés
topic Ciencias Informáticas
Parallel programming languages
Hybrid Programming
Multicore Cluster
Phylogenetic Trees
Neighbor-Joining Method
spellingShingle Ciencias Informáticas
Parallel programming languages
Hybrid Programming
Multicore Cluster
Phylogenetic Trees
Neighbor-Joining Method
Rucci, Enzo
Chichizola, Franco
Naiouf, Marcelo
De Giusti, Armando Eduardo
A Hybrid Parallel Neighbor-Joining Algorithm for Phylogenetic Tree Reconstruction on a Multicore Cluster
topic_facet Ciencias Informáticas
Parallel programming languages
Hybrid Programming
Multicore Cluster
Phylogenetic Trees
Neighbor-Joining Method
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
format Articulo
Articulo
author Rucci, Enzo
Chichizola, Franco
Naiouf, Marcelo
De Giusti, Armando Eduardo
author_facet Rucci, Enzo
Chichizola, Franco
Naiouf, Marcelo
De Giusti, Armando Eduardo
author_sort Rucci, Enzo
title A Hybrid Parallel Neighbor-Joining Algorithm for Phylogenetic Tree Reconstruction on a Multicore Cluster
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 hybrid parallel neighbor-joining algorithm for phylogenetic tree reconstruction on a multicore cluster
publishDate 2013
url http://sedici.unlp.edu.ar/handle/10915/80066
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