PRec-I-DCM3: a parallel framework for fast and accurate large-scale phylogeny reconstruction

Authors:
Yuri Dotsenko;Cristian Coarfa;Luay Nakhleh;John Mellor-Crummey;Usman Roshan
Affiliations:
Department of Computer Science, Rice University, 6100 Main Street, Houston TX 77005, USA.;Department of Computer Science, Rice University, 6100 Main Street, Houston TX 77005, USA.;Department of Computer Science, Rice University, 6100 Main Street, Houston TX 77005, USA.;Department of Computer Science, Rice University, 6100 Main Street, Houston TX 77005, USA.;Department of Computer Science, New Jersey Institute of Technology, GITC 4400, University Heights, Newark NJ 07102, USA
Venue:
International Journal of Bioinformatics Research and Applications
Year:
2006

Citing 3
Cited 1

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SODA '01 Proceedings of the twelfth annual ACM-SIAM symposium on Discrete algorithms
Solving Large Scale Phylogenetic Problems using DCM2

Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology
Rec-I-DCM3: A Fast Algorithmic Technique for Reconstructing Large Phylogenetic Trees

CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference

Phylospaces: reconstructing evolutionary trees in tuple space

IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing

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Abstract

Accurate reconstruction of phylogenetic trees often involves solving hard optimisation problems, particularly the Maximum Parsimony (MP) and Maximum Likelihood (ML) problems. Various heuristics yield good results for these problems within reasonable time only on small datasets. This is a major impediment for large-scale phylogeny reconstruction. Roshan et al. introduced Rec-I-DCM3, an efficient and accurate meta-method for solving the MP problem on large datasets of up to 14,000 taxa. We improve the performance of Rec-I-DCM3 via parallelisation. The experiments demonstrate that our parallel method, PRec-I-DCM3, achieves significant improvements, both in speed and accuracy, over its sequential counterpart.