TY - GEN
T1 - Fast phylogenetic analysis on a massively parallel machine
AU - Matsuda, Hideo
AU - Olsen, Gary J.
AU - Overbeek, Ross
AU - Kaneda, Yukio
N1 - Funding Information:
We are grateful to the Concurrent Supercomputing Consortium for access to the Intel Touchstone DIELTA System. This work was supported in part by the Japan Ministry of Education, Science and Culture under Grant in Aid for Scientific Research 04235103 and 05254209.
Publisher Copyright:
© 1994 ACM.
PY - 1994/7/16
Y1 - 1994/7/16
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85031117700&partnerID=8YFLogxK
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U2 - 10.1145/181181.181545
DO - 10.1145/181181.181545
M3 - Conference contribution
AN - SCOPUS:85031117700
T3 - Proceedings of the International Conference on Supercomputing
SP - 297
EP - 302
BT - Proceedings of the 8th International Conference on Supercomputing, ICS 1994
PB - Association for Computing Machinery
T2 - 8th International Conference on Supercomputing, ICS 1994
Y2 - 11 July 1994 through 15 July 1994
ER -