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GARD: a genetic algorithm for recombination detection

GARD: a genetic algorithm for recombination detection
GARD: a genetic algorithm for recombination detection
MOTIVATION: Phylogenetic and evolutionary inference can be severely misled if recombination is not accounted for, hence screening for it should be an essential component of nearly every comparative study. The evolution of recombinant sequences can not be properly explained by a single phylogenetic tree, but several phylogenies may be used to correctly model the evolution of non-recombinant fragments.

RESULTS: We developed a likelihood-based model selection procedure that uses a genetic algorithm to search multiple sequence alignments for evidence of recombination breakpoints and identify putative recombinant sequences. GARD is an extensible and intuitive method that can be run efficiently in parallel. Extensive simulation studies show that the method nearly always outperforms other available tools, both in terms of power and accuracy and that the use of GARD to screen sequences for recombination ensures good statistical properties for methods aimed at detecting positive selection.
1367-4803
3096-3098
Kovakovsky Pond, Sergei L.
1080b91c-2d34-4f91-a06a-2bc89f9956e0
Posada, David
ec248b95-ed62-4229-b88f-da8f2fd8e0e7
Gravenor, Michael B.
ee0d5d62-f88d-4e70-88d1-37af92cd80a4
Woelk, Christopher H.
4d3af0fd-658f-4626-b3b5-49a6192bcf7d
Frost, Simon D.W.
5f97f19b-9f1f-4e8a-9d64-01beabf0a073
Kovakovsky Pond, Sergei L.
1080b91c-2d34-4f91-a06a-2bc89f9956e0
Posada, David
ec248b95-ed62-4229-b88f-da8f2fd8e0e7
Gravenor, Michael B.
ee0d5d62-f88d-4e70-88d1-37af92cd80a4
Woelk, Christopher H.
4d3af0fd-658f-4626-b3b5-49a6192bcf7d
Frost, Simon D.W.
5f97f19b-9f1f-4e8a-9d64-01beabf0a073

Kovakovsky Pond, Sergei L., Posada, David, Gravenor, Michael B., Woelk, Christopher H. and Frost, Simon D.W. (2006) GARD: a genetic algorithm for recombination detection. Bioinformatics, 22 (24), 3096-3098. (doi:10.1093/bioinformatics/btl474). (PMID:17110367)

Record type: Article

Abstract

MOTIVATION: Phylogenetic and evolutionary inference can be severely misled if recombination is not accounted for, hence screening for it should be an essential component of nearly every comparative study. The evolution of recombinant sequences can not be properly explained by a single phylogenetic tree, but several phylogenies may be used to correctly model the evolution of non-recombinant fragments.

RESULTS: We developed a likelihood-based model selection procedure that uses a genetic algorithm to search multiple sequence alignments for evidence of recombination breakpoints and identify putative recombinant sequences. GARD is an extensible and intuitive method that can be run efficiently in parallel. Extensive simulation studies show that the method nearly always outperforms other available tools, both in terms of power and accuracy and that the use of GARD to screen sequences for recombination ensures good statistical properties for methods aimed at detecting positive selection.

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More information

e-pub ahead of print date: 3 July 2006
Published date: October 2006
Organisations: Clinical & Experimental Sciences

Identifiers

Local EPrints ID: 352763
URI: http://eprints.soton.ac.uk/id/eprint/352763
ISSN: 1367-4803
PURE UUID: 64a2785e-54d6-4a13-81ef-803c7e04bc87

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Date deposited: 17 May 2013 14:43
Last modified: 14 Mar 2024 13:55

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Contributors

Author: Sergei L. Kovakovsky Pond
Author: David Posada
Author: Michael B. Gravenor
Author: Christopher H. Woelk
Author: Simon D.W. Frost

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