Title :
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
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;
Conference_Titel :
Communications, Computers and Signal Processing, 1993., IEEE Pacific Rim Conference on
Conference_Location :
Victoria, BC
Print_ISBN :
0-7803-0971-5
DOI :
10.1109/PACRIM.1993.407169
