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

Authors:
Craig A. Stewart;David Hart;Donald K. Berry;Gary J. Olsen;Eric A. Wernert;William Fischer
Affiliations:
University Information Technology Services, Indiana University, Bloomington IN;University Information Technology Services, Indiana University, Bloomington IN;University Information Technology Services, Indiana University, Bloomington IN;University of Illinois Urbana/Champaign, Urbana, IL;University Information Technology Services, Indiana University, Bloomington IN;Indiana University, Bloomington IN
Venue:
Proceedings of the 2001 ACM/IEEE conference on Supercomputing
Year:
2001

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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.