Fast phylogenetic analysis on a massively parallel machine

Hideo Matsuda, Gary J. Olsen, Ross Overbeek, Yukio Kaneda

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

We developed a parallel processing system for analyzing phylogenetic relationships of microorganisms based on a maximum likelihood method. Methods for inferring relationships from molecular sequence data are especially valuable, given the enormous increases in DNA sequence data. The maximum likelihood method uses concrete models of the evolutionary process and are well-motivated statistically, but the computatiorwd cost has hindered the use of this method for inferring trees with more than about 20 organisms. We parallelized the maximum likelihood method by utilizing two types of parallelism, parallel evaluation of phylogenetic trees and parallel computation of likelihood values. By combining these two parallelisms, we obtained significant speedup on the Intel Touchstone DELTA.

Original languageEnglish (US)
Title of host publicationProceedings of the 8th International Conference on Supercomputing, ICS 1994
PublisherAssociation for Computing Machinery
Pages297-302
Number of pages6
ISBN (Electronic)0897916654
DOIs
StatePublished - Jul 16 1994
Event8th International Conference on Supercomputing, ICS 1994 - Manchester, United Kingdom
Duration: Jul 11 1994Jul 15 1994

Publication series

NameProceedings of the International Conference on Supercomputing
VolumePart F129421

Other

Other8th International Conference on Supercomputing, ICS 1994
CountryUnited Kingdom
CityManchester
Period7/11/947/15/94

ASJC Scopus subject areas

  • Computer Science(all)

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  • Cite this

    Matsuda, H., Olsen, G. J., Overbeek, R., & Kaneda, Y. (1994). Fast phylogenetic analysis on a massively parallel machine. In Proceedings of the 8th International Conference on Supercomputing, ICS 1994 (pp. 297-302). (Proceedings of the International Conference on Supercomputing; Vol. Part F129421). Association for Computing Machinery. https://doi.org/10.1145/181181.181545