Implementation of a parallel processing system for inference of phylogenetic trees

Author

Matsuda, Hideo ; Olsen, Gary J. ; Hagstrom, Ray ; Overbeek, Ross ; Kaneda, Yukio

Author_Institution

Dept. of Comput. & Syst. Eng., Kobe Univ., Japan

Volume

1

fYear

1993

fDate

19-21 May 1993

Firstpage

280

Abstract

A parallel processing system for inference of phylogenetic trees is reported. The trees are inferred from DNA sequence data by using a maximum likelihood method based on a stochastic model of the evolutional process. This method gives a good representation of the trees, but the computational cost has hindered the use of this method for inferring trees with more than about 20 species. By a parallel processing method based on a function partitioning approach, the authors reduced the cost significantly and obtained a phylogenetic tree of several hundred species on a massively parallel machine

Keywords

DNA; biology computing; computational complexity; evolution (biological); inference mechanisms; maximum likelihood estimation; parallel machines; stochastic processes; tree data structures; DNA sequence data; computational cost; evolutional process; function partitioning; inference of phylogenetic trees; massively parallel machine; maximum likelihood method; parallel processing system; stochastic model; Biology computing; Computational efficiency; Concurrent computing; DNA; Genetics; Mathematics; Parallel processing; Phylogeny; Systems engineering and theory; Topology;

fLanguage

English

Publisher

ieee

Conference_Titel

Communications, Computers and Signal Processing, 1993., IEEE Pacific Rim Conference on

Conference_Location

Victoria, BC

Print_ISBN

0-7803-0971-5

Type

conf

DOI

10.1109/PACRIM.1993.407169

Filename

407169