Bioinformatics Advance Access originally published online on November 16, 2006
Bioinformatics 2006 22(24):3096-3098; doi:10.1093/bioinformatics/btl474
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GARD: a genetic algorithm for recombination detection
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
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  S. S. Steiger, A. E. Fidler, J. C. Mueller, and B. Kempenaers Evidence for Adaptive Evolution of Olfactory Receptor Genes in 9 Bird Species J. Hered., December 4, 2009; (2009) esp105v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Lefebure and M. J. Stanhope Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter Genome Res., July 1, 2009; 19(7): 1224 - 1232. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. C. J. Alcantara, S. Cassol, P. Libin, K. Deforche, O. G. Pybus, M. Van Ranst, B. Galvao-Castro, A.-M. Vandamme, and T. de Oliveira A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences Nucleic Acids Res., July 1, 2009; 37(suppl_2): W634 - W642. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Goonetilleke, M. K.P. Liu, J. F. Salazar-Gonzalez, G. Ferrari, E. Giorgi, V. V. Ganusov, B. F. Keele, G. H. Learn, E. L. Turnbull, M. G. Salazar, et al. The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection J. Exp. Med., June 8, 2009; 206(6): 1253 - 1272. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. E. Smith and H. S. Malik The apolipoprotein L family of programmed cell death and immunity genes rapidly evolved in primates at discrete sites of host-pathogen interactions Genome Res., May 1, 2009; 19(5): 850 - 858. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M.-R. Abrahams, J. A. Anderson, E. E. Giorgi, C. Seoighe, K. Mlisana, L.-H. Ping, G. S. Athreya, F. K. Treurnicht, B. F. Keele, N. Wood, et al. Quantitating the Multiplicity of Infection with Human Immunodeficiency Virus Type 1 Subtype C Reveals a Non-Poisson Distribution of Transmitted Variants J. Virol., April 15, 2009; 83(8): 3556 - 3567. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Zoll, J. M. D. Galama, and F. J. M. van Kuppeveld Identification of Potential Recombination Breakpoints in Human Parechoviruses J. Virol., April 1, 2009; 83(7): 3379 - 3383. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. A. MacDuff, Z. L. Demorest, and R. S. Harris AID can restrict L1 retrotransposition suggesting a dual role in innate and adaptive immunity Nucleic Acids Res., April 1, 2009; 37(6): 1854 - 1867. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Anisimova and C. Kosiol Investigating Protein-Coding Sequence Evolution with Probabilistic Codon Substitution Models Mol. Biol. Evol., February 1, 2009; 26(2): 255 - 271. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Joos, M. Fischer, H. Kuster, S. K. Pillai, J. K. Wong, J. Boni, B. Hirschel, R. Weber, A. Trkola, H. F. Gunthard, et al. HIV rebounds from latently infected cells, rather than from continuing low-level replication PNAS, October 28, 2008; 105(43): 16725 - 16730. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|