Title :
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
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;
Conference_Titel :
Parallel and Distributed Processing Symposium, 2006. IPDPS 2006. 20th International
Print_ISBN :
1-4244-0054-6
DOI :
10.1109/IPDPS.2006.1639534
