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Building large phylogenetic trees on coarse-grained parallel machines

Keane, T.M. and Page, A.J. and Naughton, T.J. and Travers, S.A.A. and McInerney, J.O. (2005) Building large phylogenetic trees on coarse-grained parallel machines. Algorithmica. (In Press)

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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 computa- tional 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 li- cence from the system webpage at http://www.cs.nuim.ie/distributed

Item Type: Article
Keywords: bioinfomatics, distributed computing
Subjects: Science & Engineering > Computer Science
Item ID: 237
Depositing User: Andrew Page
Date Deposited: 18 Aug 2005
Journal or Publication Title: Algorithmica
Publisher: Springer
Refereed: Yes
URI:

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