Parallel implementation of a quartet-based algorithm for phylogenetic analysis

Authors:
B. B. Zhou;D. Chu;M. Tarawneh;P. Wang;C. Wang;A. Y. Zomaya;R. P. Brent
Affiliations:
School of Information Technologies, University of Sydney, NSW, Australia;School of Information Technologies, University of Sydney, NSW, Australia;School of Information Technologies, University of Sydney, NSW, Australia;School of Information Technologies, University of Sydney, NSW, Australia;School of Information Technologies, University of Sydney, NSW, Australia;School of Information Technologies, University of Sydney, NSW, Australia;Mathematical Science Institute, Australian National University, Canberra, ACT, Australia
Venue:
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
Year:
2006

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Abstract

This paper describes a parallel implementation of our recently developed algorithm for phylogenetic analysis on the IBM BlueGene/L cluster [15]. 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.