research-article

HPC selection of models of DNA substitution

Authors:

Guillermo L. Taboada,

David PosadaAuthors Info & Claims

CMSB '11: Proceedings of the 9th International Conference on Computational Methods in Systems Biology

Pages 65 - 72

https://doi.org/10.1145/2037509.2037520

Published: 21 September 2011 Publication History

Abstract

Statistical model selection has become an essential step for the estimation of phylogenies from DNA sequence alignments. The program jModelTest offers different strategies to identify best-fit models for the data at hand, but for large DNA alignments, this task can demand vast computational resources.

This paper presents a High Performance Computing (HPC) adaptation of jModelTest for shared memory multi-core systems and distributed memory cluster platforms. The performance evaluation of this HPC version on a shared memory system and on a cluster shows significant performance advantages, with speedups up to 39. This could represent a reduction in the execution time of some analyses from almost one day to half an hour.

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Digital Library

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D. Darriba, G. L. Taboada, R. Doallo, and D. Posada. Prottest 3: fast selection of best-fit models of protein evolution. Bioinformatics, 27:1164--1165, 2011.

Digital Library

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Cited By

Darriba DTaboada GDoallo RPosada D(2014)High-performance computing selection of models of DNA substitution for multicore clustersInternational Journal of High Performance Computing Applications10.1177/109434201349509528:1(112-125)Online publication date: 1-Feb-2014
https://dl.acm.org/doi/10.1177/1094342013495095
Corcoran PJacobson DBidartondo MHickey PKerekes JTaylor JJohannesson H(2012)Quantifying functional heterothallism in the pseudohomothallic ascomycete Neurospora tetraspermaFungal Biology10.1016/j.funbio.2012.06.006116:9(962-975)Online publication date: Sep-2012
https://doi.org/10.1016/j.funbio.2012.06.006

Index Terms

HPC selection of models of DNA substitution

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cover image ACM Other conferences

CMSB '11: Proceedings of the 9th International Conference on Computational Methods in Systems Biology

September 2011

224 pages

ISBN:9781450308175

DOI:10.1145/2037509

Conference Chair:
François Fages
INRIA Paris-Rocquencourt, France

Copyright © 2011 ACM.

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

Sponsors

TCSIM: IEEE Computer Society Technical Committee on Simulation
University Henri-Poincare: University Henri-Poincare - France
NVIDIA
CNRS: Centre National De La Rechercue Scientifique
Microsoft Research: Microsoft Research

In-Cooperation

SIGBio: ACM Special Interest Group on Bioinformatics

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 21 September 2011

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Xunta de Galicia (Galician Thematic Networks
European Research Council
Ministerio de Educación, Cultura y Deporte

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CMSB'11

Sponsor:

TCSIM
University Henri-Poincare
CNRS
Microsoft Research

CMSB'11: 9th International Conference on Computational Methods in Systems Biology

September 21 - 23, 2011

Paris, France

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Cited By

Darriba DTaboada GDoallo RPosada D(2014)High-performance computing selection of models of DNA substitution for multicore clustersInternational Journal of High Performance Computing Applications10.1177/109434201349509528:1(112-125)Online publication date: 1-Feb-2014
https://dl.acm.org/doi/10.1177/1094342013495095
Corcoran PJacobson DBidartondo MHickey PKerekes JTaylor JJohannesson H(2012)Quantifying functional heterothallism in the pseudohomothallic ascomycete Neurospora tetraspermaFungal Biology10.1016/j.funbio.2012.06.006116:9(962-975)Online publication date: Sep-2012
https://doi.org/10.1016/j.funbio.2012.06.006

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