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
Proceedings of the Fifth IEEE International Workshop
on High Performance Computational Biology (HiCOMB06),
Rhodes, Greece, April 2006, 8 pp. Proceedings published on CDROM.
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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