Fast phylogenetic analysis on a massively parallel machine

  • Authors:

  • Hideo Matsuda;Gary J. Olsen;Ross Overbeek;Yukio Kaneda

  • Affiliations:

  • Department of Computer and Systems Engineering, Faculty of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657, Japan;Department of Microbiology, University of Illinois, Urbana, IL;Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL;Department of Computer and Systems Engineering, Faculty of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657, Japan

  • Venue:
  • ICS '94 Proceedings of the 8th international conference on Supercomputing
  • Year:
  • 1994

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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 computational 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.