Implementation of a parallel processing system for inference of phylogenetic trees

Hideo Matsuda, Gary J Olsen, Ray Hagstrom, Ross Overbeek, Yukio Kaneda

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

Abstract

This paper reports a parallel processing system for inference of phylogenetic trees. The trees are inferred from DNA sequence data by using a maximum likelihood method based on a stochastic model of the evolutional process. This method gives a good representation of the trees, but the computational cost has hindered the use of this method for inferring trees with more than about 20 species. By a parallel processing method based on a function partitioning approach, we achieved to reduce the cost significantly and obtained the phylogenetic tree of several hundreds of species on a massively parallel machine.

Original languageEnglish (US)
Title of host publicationIEEE Pac Rim Conf Commun Comput Signal Process
PublisherPubl by IEEE
Pages280-283
Number of pages4
ISBN (Print)0780312198
StatePublished - 1993
Externally publishedYes
EventProceedings of the IEEE 1993 Pacific Rim Conference on Communications, Computers and Signal Processing - Victoria, BC, Can
Duration: May 19 1993May 21 1993

Other

OtherProceedings of the IEEE 1993 Pacific Rim Conference on Communications, Computers and Signal Processing
CityVictoria, BC, Can
Period5/19/935/21/93

ASJC Scopus subject areas

  • Engineering(all)

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  • Cite this

    Matsuda, H., Olsen, G. J., Hagstrom, R., Overbeek, R., & Kaneda, Y. (1993). Implementation of a parallel processing system for inference of phylogenetic trees. In IEEE Pac Rim Conf Commun Comput Signal Process (pp. 280-283). Publ by IEEE.