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Building Large Phylogenetic Trees on Coarse-Grained Parallel Machines

Keane, Thomas and Page, Andrew and Naughton, Thomas and Travers, Simon and McInerney, James (2006) Building Large Phylogenetic Trees on Coarse-Grained Parallel Machines. Algorithmica, 45 (3). pp. 285-300.

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Abstract

Abstract Phylogenetic analysis is an area of computational biology concerned with the reconstruction of evolutionary relationships between organisms, genes, and gene families. Maximum likelihood evaluation has proven to be one of the most reliable methods for constructing phylogenetic trees. The huge computational requirements associated with maximum likelihood analysis means that it is not feasible to produce large phylogenetic trees using a single processor. We have completed a fully cross platform coarse-grained distributed application, DPRml, which overcomes many of the limitations imposed by the current set of parallel phylogenetic programs. We have completed a set of efficiency tests that show how to maximise efficiency while using the program to build large phylogenetic trees. The software is publicly available under the terms of the GNU general public licence from the system webpage at http://www.cs.nuim.ie/distributed.

Item Type: Article
Keywords: Distributed computing; Bioinformatics; Phylogenetic Trees; Maximun likelihood;
Subjects: Science & Engineering > Biology
Item ID: 917
Depositing User: Dr. James McInerney
Date Deposited: 26 Feb 2008
Journal or Publication Title: Algorithmica
Publisher: Springer
Refereed: Yes
URI:

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