Parallel Implementation and Performance of FastDNAml - A Program for Maximum Likelihood Phylogenetic Inference

Author

Stewart, C.A. ; Hart, D. ; Berry, D.K. ; Olsen, G.J. ; Wernert, E.A. ; Fischer, W.

Author_Institution

Indiana University

fYear

2001

fDate

10-16 Nov. 2001

Firstpage

32

Lastpage

32

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.

Keywords

Phylogenetics; bioinformatics; maximum likelihood; parallel applications; scalability; Availability; Bifurcation; Bioinformatics; Concurrent computing; DNA; Organisms; Phylogeny; Scalability; Sequences; Testing; Phylogenetics; bioinformatics; maximum likelihood; parallel applications; scalability;

fLanguage

English

Publisher

ieee

Conference_Titel

Supercomputing, ACM/IEEE 2001 Conference

Conference_Location

Denver, CO, USA

Print_ISBN

1-58113-293-X

Type

conf

DOI

10.1109/SC.2001.10001

Filename

1592808