Parallel implementation of a quartet-based algorithm for phylogenetic analysis

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

doi:10.1109/IPDPS.2006.1639534

Parallel implementation of a quartet-based algorithm for phylogenetic analysis

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

^*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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.

Original language	English
Title of host publication	20th International Parallel and Distributed Processing Symposium, IPDPS 2006
Publisher	IEEE Computer Society
ISBN (Print)	1424400546, 9781424400546
DOIs	https://doi.org/10.1109/IPDPS.2006.1639534
Publication status	Published - 2006
Event	20th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2006 - Rhodes Island, Greece Duration: 25 Apr 2006 → 29 Apr 2006

Publication series

Name	20th International Parallel and Distributed Processing Symposium, IPDPS 2006
Volume	2006

Conference

Conference	20th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2006
Country/Territory	Greece
City	Rhodes Island
Period	25/04/06 → 29/04/06

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10.1109/IPDPS.2006.1639534

Cite this

Zhou, B. B., Chu, D., Tarawneh, M., Wang, P., Wang, C., Zomaya, A. Y., & Brent, R. P. (2006). Parallel implementation of a quartet-based algorithm for phylogenetic analysis. In 20th International Parallel and Distributed Processing Symposium, IPDPS 2006 Article 1639534 (20th International Parallel and Distributed Processing Symposium, IPDPS 2006; Vol. 2006). IEEE Computer Society. https://doi.org/10.1109/IPDPS.2006.1639534

@inproceedings{24a0c241936d40668a7f8fb33cdc17b7,

title = "Parallel implementation of a quartet-based algorithm for phylogenetic analysis",

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.",

author = "Zhou, {B. B.} and D. Chu and M. Tarawneh and P. Wang and C. Wang and Zomaya, {A. Y.} and Brent, {R. P.}",

year = "2006",

doi = "10.1109/IPDPS.2006.1639534",

language = "English",

isbn = "1424400546",

series = "20th International Parallel and Distributed Processing Symposium, IPDPS 2006",

publisher = "IEEE Computer Society",

booktitle = "20th International Parallel and Distributed Processing Symposium, IPDPS 2006",

address = "United States",

note = "20th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2006 ; Conference date: 25-04-2006 Through 29-04-2006",

}

Zhou, BB, Chu, D, Tarawneh, M, Wang, P, Wang, C, Zomaya, AY & Brent, RP 2006, Parallel implementation of a quartet-based algorithm for phylogenetic analysis. in 20th International Parallel and Distributed Processing Symposium, IPDPS 2006., 1639534, 20th International Parallel and Distributed Processing Symposium, IPDPS 2006, vol. 2006, IEEE Computer Society, 20th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2006, Rhodes Island, Greece, 25/04/06. https://doi.org/10.1109/IPDPS.2006.1639534

Parallel implementation of a quartet-based algorithm for phylogenetic analysis. / Zhou, B. B.; Chu, D.; Tarawneh, M. et al.
20th International Parallel and Distributed Processing Symposium, IPDPS 2006. IEEE Computer Society, 2006. 1639534 (20th International Parallel and Distributed Processing Symposium, IPDPS 2006; Vol. 2006).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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T1 - Parallel implementation of a quartet-based algorithm for phylogenetic analysis

AU - Zhou, B. B.

AU - Chu, D.

AU - Tarawneh, M.

AU - Wang, P.

AU - Wang, C.

AU - Zomaya, A. Y.

AU - Brent, R. P.

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AB - 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.

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DO - 10.1109/IPDPS.2006.1639534

M3 - Conference contribution

SN - 1424400546

SN - 9781424400546

T3 - 20th International Parallel and Distributed Processing Symposium, IPDPS 2006

BT - 20th International Parallel and Distributed Processing Symposium, IPDPS 2006

PB - IEEE Computer Society

T2 - 20th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2006

Y2 - 25 April 2006 through 29 April 2006

ER -

Zhou BB, Chu D, Tarawneh M, Wang P, Wang C, Zomaya AY et al. Parallel implementation of a quartet-based algorithm for phylogenetic analysis. In 20th International Parallel and Distributed Processing Symposium, IPDPS 2006. IEEE Computer Society. 2006. 1639534. (20th International Parallel and Distributed Processing Symposium, IPDPS 2006). doi: 10.1109/IPDPS.2006.1639534

Parallel implementation of a quartet-based algorithm for phylogenetic analysis

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