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A hybrid parallel neighbor-joining algorithm for phylogenetic tree reconstruction on a multicore cluster

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Rucci, Enzo

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Material type: Article

ArticlePublication details: ref_localidad@NULL : American V-King Scientific Publishing, 2013Description: 1 archivo (192,2 KB)Subject(s):

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Summary: 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.

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Item type	Current library	Call number	Status	Date due	Barcode
Capítulo de libro	Biblioteca Fac.Informática	A0455 (Browse shelf(Opens below))	Available		DIF-A0455

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Formato de archivo: PDF. -- Este documento es producción intelectual de la Facultad de Informática - UNLP (Colección BIPA/Biblioteca)

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.

Parallel & Cloud Computing, 2(3), pp. 74-80

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