Parallel Implementation of a Quartet-based Algorithm

222. B. B. Zhou, D. Chu, M. Tarawneh, P. Wang, C. Wang, A. Y. Zomaya and R. P. Brent, Parallel implementation of a quartet-based algorithm for phylogenetic analysis, Proceedings of the Fifth IEEE International Workshop on High Performance Computational Biology (HiCOMB06), Rhodes, Greece, April 2006, 8 pp. Proceedings published on CDROM.

Preprint: pdf (240K).


This paper describes a parallel implementation of our recently developed algorithm for phylogenetic analysis on the IBM BlueGene/L cluster [IBM J. Research and Development 49, 2/3 (2005)]. This algorithm constructs evolutionary trees for a given set of DNA or protein sequences based on the topology of every possible quartet tree. Our experimental results show 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.

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