Skip Navigation


Bioinformatics Advance Access originally published online on November 16, 2006
Bioinformatics 2006 22(24):3096-3098; doi:10.1093/bioinformatics/btl474
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
22/24/3096    most recent
btl474v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Kosakovsky Pond, S. L.
Right arrow Articles by Frost, S. D.W.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Kosakovsky Pond, S. L.
Right arrow Articles by Frost, S. D.W.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

GARD: a genetic algorithm for recombination detection

Sergei L. Kosakovsky Pond *, David Posada 1, Michael B. Gravenor 2, Christopher H. Woelk and Simon D.W. Frost

Department of Pathology, University of California San Diego La Jolla, CA 92093, USA
1 Departamento de Bioquímica, Genética e Inmunología Facultad de Biología, Universidad de Vigo, Vigo 36310, Spain
2 School of Medicine, University of Wales Swansea, UK

*To whom correspondence should be addressed.

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.

Availability: Freely available http://www.datamonkey.org/GARD/

Contact: spond{at}ucsd.edu

Received on July 3, 2006; accepted on September 2, 2006

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 J. Virol.Home page
G. Palacios, J. Hui, P. L. Quan, A. Kalkstein, K. S. Honkavuori, A. V. Bussetti, S. Conlan, J. Evans, Y. P. Chen, D. vanEngelsdorp, et al.
Genetic Analysis of Israel Acute Paralysis Virus: Distinct Clusters Are Circulating in the United States
J. Virol., July 1, 2008; 82(13): 6209 - 6217.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
C.-C. Hon, T.-Y. Lam, Z.-L. Shi, A. J. Drummond, C.-W. Yip, F. Zeng, P.-Y. Lam, and F. C.-C. Leung
Evidence of the Recombinant Origin of a Bat Severe Acute Respiratory Syndrome (SARS)-Like Coronavirus and Its Implications on the Direct Ancestor of SARS Coronavirus
J. Virol., February 15, 2008; 82(4): 1819 - 1826.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
C. M. Noviello, S. L. K. Pond, M. J. Lewis, D. D. Richman, S. K. Pillai, O. O. Yang, S. J. Little, D. M. Smith, and J. C. Guatelli
Maintenance of Nef-Mediated Modulation of Major Histocompatibility Complex Class I and CD4 after Sexual Transmission of Human Immunodeficiency Virus Type 1
J. Virol., May 1, 2007; 81(9): 4776 - 4786.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.