Article

Parallel implementation and performance of fastDNAml: a program for maximum likelihood phylogenetic inference

Authors:

Craig A. Stewart,

Donald K. Berry,

Eric A. Wernert,

William FischerAuthors Info & Claims

SC '01: Proceedings of the 2001 ACM/IEEE conference on Supercomputing

Page 20

https://doi.org/10.1145/582034.582054

Published: 10 November 2001 Publication History

Abstract

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.

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cover image ACM Conferences

SC '01: Proceedings of the 2001 ACM/IEEE conference on Supercomputing

November 2001

756 pages

ISBN:158113293X

DOI:10.1145/582034

Conference Chair:
Charles Slocomb
Los Alamos National Laboratory

Copyright © 2001 ACM.

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Published: 10 November 2001

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SC '01: International Conference for High Performance Computing, Networking, Storage and Analysis

November 10 - 16, 2001

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