Parallel implementation of a quartet-based algorithm for phylogenetic analysis

Author

Zhou, B.B. ; Chu, D. ; Tarawneh, M. ; Wang, P. ; Wang, C. ; Zomaya, A.Y. ; Brent, R.P.

Author_Institution

Sch. of Inf. Technol., Sydney Univ., NSW, Australia

fYear

2006

fDate

25-29 April 2006

Abstract

This paper describes a parallel implementation of our recently developed algorithm for phylogenetic analysis on the IBM BlueGene/L cluster. This algorithm constructs evolutionary trees for a given set of DNA or protein sequences based on the topological information of every possible quartet trees. Our experimental results showed that it has several advantages over many popular algorithms. By distributing the quartet weights evenly across the processing nodes and making effective use of a fast collective network on the IBM BlueGene/L cluster, we are able to achieve a close to linear speedup even when the number of processors involved in the computation is large.

Keywords

DNA; biology computing; evolutionary computation; parallel processing; proteins; trees (mathematics); DNA; IBM BlueGene/L cluster; evolutionary tree; parallel implementation; phylogenetic analysis; protein sequence; quartet-based algorithm; Algorithm design and analysis; Australia; Clustering algorithms; Computer networks; Distributed computing; Information analysis; Information technology; Phylogeny; Sequences; Topology;

fLanguage

English

Publisher

ieee

Conference_Titel

Parallel and Distributed Processing Symposium, 2006. IPDPS 2006. 20th International

Print_ISBN

1-4244-0054-6

Type

conf

DOI

10.1109/IPDPS.2006.1639534

Filename

1639534