Bioinformatics Advance Access originally published online on September 17, 2004
Bioinformatics 2005 21(2):260-262; doi:10.1093/bioinformatics/bth490
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Bioinformatics vol. 21 issue 2 © Oxford University Press 2005; all rights reserved.
RDP2: recombination detection and analysis from sequence alignments
1 Institute of Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town 7000, South Africa
2 Department of Biochemistry, Genetics and Immunology, University of Vigo 36200 Vigo, Spain
*To whom correspondence should be addressed.
Summary: RDP2 is a Windows 95/XP program that examines nucleotide sequence alignments and attempts to identify recombinant sequences and recombination breakpoints using 10 published recombination detection methods, including GENECONV, BOOTSCAN, MAXIMUM 
2, CHIMAERA and SISTER SCANNING. The program enables fast automated analysis of large alignments (up to 300 sequences containing 13 000 sites), and interactive exploration, management and verification of results with different recombination detection and tree drawing methods.
Availability: RDP2 is available free from the RDP2 website (http://darwin.uvigo.es/rdp/rdp.html)
Contact: darren{at}science.uct.ac.za
Supplementary information: Detailed descriptions of RDP2 and the methods it implements are included in the program manual, which can be downloaded from the RDP2 website.
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C. M. Barr, S. R. Keller, P. K. Ingvarsson, D. B. Sloan, and D. R. Taylor Variation in Mutation Rate and Polymorphism Among Mitochondrial Genes of Silene vulgaris Mol. Biol. Evol., August 1, 2007; 24(8): 1783 - 1791. [Abstract] [Full Text] [PDF]
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X. Bailly, I. Olivieri, B. Brunel, J.-C. Cleyet-Marel, and G. Bena Horizontal Gene Transfer and Homologous Recombination Drive the Evolution of the Nitrogen-Fixing Symbionts of Medicago Species J. Bacteriol., July 15, 2007; 189(14): 5223 - 5236. [Abstract] [Full Text] [PDF]
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F. L. Thompson, B. Gomez-Gil, A. T. R. Vasconcelos, and T. Sawabe Multilocus Sequence Analysis Reveals that Vibrio harveyi and V. campbellii Are Distinct Species Appl. Envir. Microbiol., July 1, 2007; 73(13): 4279 - 4285. [Abstract] [Full Text] [PDF]
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J. A. Willment, D. P. Martin, K. E. Palmer, W. H. Schnippenkoetter, D. N. Shepherd, and E. P. Rybicki Identification of long intergenic region sequences involved in maize streak virus replication J. Gen. Virol., June 1, 2007; 88(6): 1831 - 1841. [Abstract] [Full Text] [PDF]
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J. Syring, K. Farrell, R. Businsky, R. Cronn, and A. Liston Widespread Genealogical Nonmonophyly in Species of Pinus Subgenus Strobus Syst Biol, April 1, 2007; 56(2): 163 - 181. [Abstract] [Full Text] [PDF]
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J. A. Castillo and J. T. Greenberg Evolutionary Dynamics of Ralstonia solanacearum Appl. Envir. Microbiol., February 15, 2007; 73(4): 1225 - 1238. [Abstract] [Full Text] [PDF]
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K. Ohshima, Y. Tomitaka, J. T. Wood, Y. Minematsu, H. Kajiyama, K. Tomimura, and A. J. Gibbs Patterns of recombination in turnip mosaic virus genomic sequences indicate hotspots of recombination J. Gen. Virol., January 1, 2007; 88(1): 298 - 315. [Abstract] [Full Text] [PDF]
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L. Heath, E. van der Walt, A. Varsani, and D. P. Martin Recombination Patterns in Aphthoviruses Mirror Those Found in Other Picornaviruses J. Virol., December 1, 2006; 80(23): 11827 - 11832. [Abstract] [Full Text] [PDF]
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W. Ren, W. Li, M. Yu, P. Hao, Y. Zhang, P. Zhou, S. Zhang, G. Zhao, Y. Zhong, S. Wang, et al. Full-length genome sequences of two SARS-like coronaviruses in horseshoe bats and genetic variation analysis. J. Gen. Virol., November 1, 2006; 87(Pt 11): 3355 - 3359. [Abstract] [Full Text] [PDF]
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L. Baldo, J. C. Dunning Hotopp, K. A. Jolley, S. R. Bordenstein, S. A. Biber, R. R. Choudhury, C. Hayashi, M. C. J. Maiden, H. Tettelin, and J. H. Werren Multilocus Sequence Typing System for the Endosymbiont Wolbachia pipientis Appl. Envir. Microbiol., November 1, 2006; 72(11): 7098 - 7110. [Abstract] [Full Text] [PDF]
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R. Gray, C. Mulligan, B. Molini, E. Sun, L Giacani, C Godornes, A Kitchen, S. Lukehart, and A Centurion-Lara Molecular Evolution of the tprC, D, I, K, G, and J Genes in the Pathogenic Genus Treponema Mol. Biol. Evol., November 1, 2006; 23(11): 2220 - 2233. [Abstract] [Full Text] [PDF]
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K. Scheffler, D. P. Martin, and C. Seoighe Robust inference of positive selection from recombining coding sequences Bioinformatics, October 15, 2006; 22(20): 2493 - 2499. [Abstract] [Full Text] [PDF]
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I. Keller, I. C. Chintauan-Marquier, P. Veltsos, and R. A. Nichols Ribosomal DNA in the Grasshopper Podisma pedestris: Escape From Concerted Evolution Genetics, October 1, 2006; 174(2): 863 - 874. [Abstract] [Full Text] [PDF]
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P. Buendia and G. Narasimhan Serial NetEvolve: a flexible utility for generating serially-sampled sequences along a tree or recombinant network Bioinformatics, September 15, 2006; 22(18): 2313 - 2314. [Abstract] [Full Text] [PDF]
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A. Varsani, E. van der Walt, L. Heath, E. P. Rybicki, A. L. Williamson, and D. P. Martin Evidence of ancient papillomavirus recombination J. Gen. Virol., September 1, 2006; 87(9): 2527 - 2531. [Abstract] [Full Text] [PDF]
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U. Nubel, R. Reissbrodt, A. Weller, R. Grunow, M. Porsch-Ozcurumez, H. Tomaso, E. Hofer, W. Splettstoesser, E.-J. Finke, H. Tschape, et al. Population Structure of Francisella tularensis. J. Bacteriol., July 1, 2006; 188(14): 5319 - 5324. [Abstract] [Full Text] [PDF]
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M. Zhang, A.-K. Schultz, C. Calef, C. Kuiken, T. Leitner, B. Korber, B. Morgenstern, and M. Stanke jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1. Nucleic Acids Res., July 1, 2006; 34(suppl_2): W463 - W465. [Abstract] [Full Text] [PDF]
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K. Rebenstorf, T. Candresse, M. J. Dulucq, C. Buttner, and C. Obermeier Host Species-Dependent Population Structure of a Pollen-Borne Plant Virus, Cherry Leaf Roll Virus J. Virol., March 1, 2006; 80(5): 2453 - 2462. [Abstract] [Full Text] [PDF]
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C. L. Nesbo, M. Dlutek, and W. F. Doolittle Recombination in Thermotoga: Implications for Species Concepts and Biogeography Genetics, February 1, 2006; 172(2): 759 - 769. [Abstract] [Full Text] [PDF]
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L. Baldo, S. Bordenstein, J. J. Wernegreen, and J. H. Werren Widespread Recombination Throughout Wolbachia Genomes Mol. Biol. Evol., February 1, 2006; 23(2): 437 - 449. [Abstract] [Full Text] [PDF]
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