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Proceedings of the 2001 ACM/IEEE conference on Supercomputing
Parallel Implementation and Performance of FastDNAml — A Program for Maximum Likelihood Phylogenetic Inference
Denver, Colorado
November 10-November 16
ISBN: 1-58113-293-X
Craig A. Stewart, Indiana University
David Hart, Indiana University
Donald K. Berry, Indiana University
Gary J. Olsen, University of Illinois Urbana/Champaign
Eric A. Wernert, Indiana University
William Fischer, Indiana University
This paper describes the parallel implementation of fastDNAml, a program for the maximum likelihood inference of phylogenetic trees from DNA sequence data. Mathematical means of inferring phylogenetic trees have been made possible by the wealth of DNA data now available. Maximum likelihood analysis of phylogenetic trees is extremely computationally intensive. Availability of computer resources is a key factor limiting use of such analyses. fastDNAml is implemented in serial, PVM, and MPI versions, and may be modified to use other message passing libraries in the future. We have developed a viewer for comparing phylogenies. We tested the scaling behavior of fastDNAml on an IBM RS/6000 SP up to 64 processors. The parallel version of fastDNAml is one of very few computational phylogenetics codes that scale well. fastDNAml is available for download as source code or compiled for Linux or AIX.
Index Terms:
Phylogenetics, bioinformatics, maximum likelihood, parallel applications, scalability
Citation:
Craig A. Stewart, David Hart, Donald K. Berry, Gary J. Olsen, Eric A. Wernert, William Fischer, "Parallel Implementation and Performance of FastDNAml — A Program for Maximum Likelihood Phylogenetic Inference," sc, pp.32, Proceedings of the 2001 ACM/IEEE conference on Supercomputing, 2001
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