NDLI: PRec-I-DCM3: A Parallel Framework for Fast and Accurate Large Scale Phylogeny Reconstruction

Content Provider	IEEE Xplore Digital Library
Author	Coarfa, C. Dotsenko, Y. Mellor-Crummey, J. Nakhleh, L. Roshan, U.
Copyright Year	2005
Description	Author affiliation: Rice Univ., Houston, TX (Coarfa, C.; Dotsenko, Y.; Mellor-Crummey, J.; Nakhleh, L.)
Abstract	Accurate reconstruction of phylogenetic trees very often involves solving hard optimization problems, particularly the maximum parsimony (MP) and maximum likelihood (ML) problems. Various heuristics have been devised for solving these two problems; however, they obtain good results within reasonable time only on small datasets. This has been a major impediment for large-scale phylogeny reconstruction, particularly for the effort to assemble the Tree of Life - the evolutionary relationship of all organisms on earth. Roshan et al. recently introduced Rec-I-DCM3, an efficient and accurate meta-method for solving the MP problem on large datasets of up to 14,000 taxa. Nonetheless, a drastic improvement in Rec-I-DCM3's performance is still needed in order to achieve similar (or better) accuracy on datasets at the scale of the Tree of Life. In this paper, we improve the performance of Rec-I-DCM3 via parallelization. Experimental results demonstrate that our parallel method, PRec-I-DCM3, achieves significant improvements, both in speed and accuracy, over its sequential counterpart
Sponsorship	IEEE Comput. Soc. TCDP and TCPP Fukuoka Inst. of Technol. (FIT)
Starting Page	346
Ending Page	350
File Size	203657
Page Count	5
File Format	PDF
ISBN	0769522815
ISSN	15219097
DOI	10.1109/ICPADS.2005.240
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2005-07-20
Publisher Place	Japan
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Large-scale systems Phylogeny Algorithm design and analysis Organisms Earth Biology computing Data analysis Polynomials Impedance Assembly
Content Type	Text
Resource Type	Article
Subject	Hardware and Architecture

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