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.
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Abstract |
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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.
A major problem encountered while using standard phylogenetic methods in studies involving recombining organisms is that the evolutionary history of a recombinant sequence cannot be described with a single phylogenetic tree. A single recombinant sequence in an alignment can seriously influence the branching order and branch lengths of the phylogenetic trees constructed using the alignment (Posada and Crandall, 2002). In addition, recombination compromises the validity of several phylogenetic inferences one can make by examining trees (Schierup and Hein, 2000a,b. A number of computational tools for detecting and quantifying various aspects of recombination have therefore been developed (for a list of available recombination detection programs see http://www.umber.embnet.org/~robertson/recombination/index.shtml). A Comparison of the recombination detection power of 14 of these methods using simulated and real datasets indicated that while some always performed better than others, no single method can be adjudged to be best in detecting recombination under all conditions (Posada and Crandall, 2001; Posada, 2000).
Sharing major components of its user interface and the RDP recombination detection method with its predecessor, RDP, RDP2 implements a variety of additional non-parametric recombination detection methods (i.e. methods that do not make use of population genetic models and make no attempt to estimate the population recombination rate; Table 1). Among the new inclusions are many methods that have performed well in comparative tests (Drouin et al., 1999; Posada and Crandall, 2001; Posada, 2000). We have focused on published methods that can be used to (1) identify recombinant sequences, (2) identify recombination breakpoints and (3) identify parental sequences. The program can use any combination of six methods to automatically (RDP, GENECONV, MAXIMUM 2, BOOTSCAN, CHIMAERA and SISTER SCANNING) identify recombinant and parental sequences, estimate breakpoint positions and calculate probability scores for potential recombination events. Once all potential recombination events are identified, RDP2 sorts analysis results and attempts to determine the number of unique recombination events identifiable in an alignment. RDP2 can be set to automatically (1) filter out unique events detected by fewer than a specified number of methods, (2) identify consensus daughter and parental sequences using all evidence for a single actual recombination event (often involving many potential parental and daughter sequence combinations detected using multiple methods) and (3) use all evidence for a single actual event to determine most probable breakpoint positions using a modified maximum 2 approach (Maynard-Smith, 1992).
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RDP2 permits exploration and checking of analysis results in a highly interactive and user-friendly way. For any detected recombinations event, informations such as the method used to detect the event, breakpoint positions, parental sequences, probability values, degrees of agreement with results obtained using other detection methods, raw plot data, informative sites in the alignment and phylogenetic trees, can be displayed by simply clicking on a graphical representation of the event. Once an event is selected for more detailed study, checking the evidence for recombination using 10 different recombination detection methods (besides the six automated methods these also include LARD, TOPAL, RETICULATE and DISTANCE PLOTS) is achieved by simply selecting the methods from a menu. To further aid in evaluating evidence for recombination, RDP2 can also use PHYLIP components simultaneously (Felsenstein, 1989, Olsen et al., 1994) to display phylogenetic trees (UPGMA, bootstrapped neighbor-joining, least squares or maximum-likelihood) constructed from different portions of an alignment.
As the amount of detectable recombination in an alignment increases, the complexity of correctly inferring which sequences are parental and which are recombinant increases as well. RDP2 encourages user verification of its analysis results and permits user acceptance and rejection of potential recombination events (useful for tracking the progress of an analysis), and interactive ‘correction’ of apparent parental and daughter sequence misidentification.
We have not placed any restrictions on the size of alignments that can be examined using RDP2. For example, automated analyses using all the detection methods together on a PC with 256 MB RAM and a 1 GHz Celeron Processor can take 5 min for a 50 sequence alignment of 3 kb long sequences and less than 48 h for a 316 sequence alignment of 13 kb long sequences.
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Acknowledgments |
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We would like to thank Stanley Sawyer, Andrew Rambaut, Ingrid Jakobsen, Joseph Felsenstein, Gary Olsen, Adrian Gibbs and John Armstrong for either agreeing to have their programs distributed using RDP2 or providing pieces of code in RDP2. We also thank The National Research Foundation of South Africa (D.P.M.), US National Institutes of Health (D.P.) and the ‘Ramón y Cajal’ programme of the Spanish government (D.P.) for partially funding the development and distribution of RDP2.
Received on April 20, 2004; revised on June 28, 2004; accepted on August 13, 2004
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Y. Moran, H. Weinberger, J. C. Sullivan, A. M. Reitzel, J. R. Finnerty, and M. Gurevitz Concerted Evolution of Sea Anemone Neurotoxin Genes Is Revealed through Analysis of the Nematostella vectensis Genome Mol. Biol. Evol., April 1, 2008; 25(4): 737 - 747. [Abstract] [Full Text] [PDF]
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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]
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A. N. Lukashev, O. E. Ivanova, T. P. Eremeeva, and R. D. Iggo Evidence of frequent recombination among human adenoviruses J. Gen. Virol., February 1, 2008; 89(2): 380 - 388. [Abstract] [Full Text] [PDF]
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L. Lu, D. Murphy, C. Li, S. Liu, X. Xia, P. H. Pham, Y. Jin, C. H. Hagedorn, and K. Abe Complete genomes of three subtype 6t isolates and analysis of many novel hepatitis C virus variants within genotype 6 J. Gen. Virol., February 1, 2008; 89(2): 444 - 452. [Abstract] [Full Text] [PDF]
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B. Cardazzo, E. Negrisolo, L. Carraro, L. Alberghini, T. Patarnello, and V. Giaccone Multiple-Locus Sequence Typing and Analysis of Toxin Genes in Bacillus cereus Food-Borne Isolates Appl. Envir. Microbiol., February 1, 2008; 74(3): 850 - 860. [Abstract] [Full Text] [PDF]
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D. Penny, W. T. White, M. D. Hendy, and M. J. Phillips A Bias in ML Estimates of Branch Lengths in the Presence of Multiple Signals Mol. Biol. Evol., February 1, 2008; 25(2): 239 - 242. [Abstract] [Full Text] [PDF]
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S. Duffy and E. C. Holmes Phylogenetic Evidence for Rapid Rates of Molecular Evolution in the Single-Stranded DNA Begomovirus Tomato Yellow Leaf Curl Virus J. Virol., January 15, 2008; 82(2): 957 - 965. [Abstract] [Full Text] [PDF]
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C. Ha, S. Coombs, P. Revill, R. Harding, M. Vu, and J. Dale Molecular characterization of begomoviruses and DNA satellites from Vietnam: additional evidence that the New World geminiviruses were present in the Old World prior to continental separation J. Gen. Virol., January 1, 2008; 89(1): 312 - 326. [Abstract] [Full Text] [PDF]
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L. A. Shackelton, K. Hoelzer, C. R. Parrish, and E. C. Holmes Comparative analysis reveals frequent recombination in the parvoviruses J. Gen. Virol., December 1, 2007; 88(12): 3294 - 3301. [Abstract] [Full Text] [PDF]
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J. Aaskov, K. Buzacott, E. Field, K. Lowry, A. Berlioz-Arthaud, and E. C. Holmes Multiple recombinant dengue type 1 viruses in an isolate from a dengue patient J. Gen. Virol., December 1, 2007; 88(12): 3334 - 3340. [Abstract] [Full Text] [PDF]
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P. Lefeuvre, D. P. Martin, M. Hoareau, F. Naze, H. Delatte, M. Thierry, A. Varsani, N. Becker, B. Reynaud, and J.-M. Lett Begomovirus 'melting pot' in the south-west Indian Ocean islands: molecular diversity and evolution through recombination J. Gen. Virol., December 1, 2007; 88(12): 3458 - 3468. [Abstract] [Full Text] [PDF]
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J. Bannoehr, N. L. Ben Zakour, A. S. Waller, L. Guardabassi, K. L. Thoday, A. H. M. van den Broek, and J. R. Fitzgerald Population Genetic Structure of the Staphylococcus intermedius Group: Insights into agr Diversification and the Emergence of Methicillin-Resistant Strains J. Bacteriol., December 1, 2007; 189(23): 8685 - 8692. [Abstract] [Full Text] [PDF]
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F. Hmaied, F. Legrand-Abravanel, F. Nicot, N. Garrigues, S. Chapuy-Regaud, M. Dubois, R. Njouom, J. Izopet, and C. Pasquier Full-length genome sequences of hepatitis C virus subtype 4f J. Gen. Virol., November 1, 2007; 88(11): 2985 - 2990. [Abstract] [Full Text] [PDF]
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B. E. Owor, D. P. Martin, D. N. Shepherd, R. Edema, A. L. Monjane, E. P. Rybicki, J. A. Thomson, and A. Varsani Genetic analysis of maize streak virus isolates from Uganda reveals widespread distribution of a recombinant variant J. Gen. Virol., November 1, 2007; 88(11): 3154 - 3165. [Abstract] [Full Text] [PDF]
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Y. Tanabe, F. Kasai, and M. M. Watanabe Multilocus sequence typing (MLST) reveals high genetic diversity and clonal population structure of the toxic cyanobacterium Microcystis aeruginosa Microbiology, November 1, 2007; 153(11): 3695 - 3703. [Abstract] [Full Text] [PDF]
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L. Diancourt, V. Passet, C. Chervaux, P. Garault, T. Smokvina, and S. Brisse Multilocus Sequence Typing of Lactobacillus casei Reveals a Clonal Population Structure with Low Levels of Homologous Recombination Appl. Envir. Microbiol., October 15, 2007; 73(20): 6601 - 6611. [Abstract] [Full Text] [PDF]
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L. B. Thackray, C. E. Wobus, K. A. Chachu, B. Liu, E. R. Alegre, K. S. Henderson, S. T. Kelley, and H. W. Virgin IV Murine Noroviruses Comprising a Single Genogroup Exhibit Biological Diversity despite Limited Sequence Divergence J. Virol., October 1, 2007; 81(19): 10460 - 10473. [Abstract] [Full Text] [PDF]
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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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X. Wu, Z. Cai, X.-F. Wan, T. Hoang, R. Goebel, and G. Lin Nucleotide composition string selection in HIV-1 subtyping using whole genomes Bioinformatics, July 15, 2007; 23(14): 1744 - 1752. [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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L. Lu, C. Li, Y. Fu, L. Thaikruea, S. Thongswat, N. Maneekarn, C. Apichartpiyakul, H. Hotta, H. Okamoto, D. Netski, et al. Complete genomes for hepatitis C virus subtypes 6f, 6i, 6j and 6m: viral genetic diversity among Thai blood donors and infected spouses J. Gen. Virol., May 1, 2007; 88(5): 1505 - 1518. [Abstract] [Full Text] [PDF]
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F. Legrand-Abravanel, J. Claudinon, F. Nicot, M. Dubois, S. Chapuy-Regaud, K. Sandres-Saune, C. Pasquier, and J. Izopet New Natural Intergenotypic (2/5) Recombinant of Hepatitis C Virus J. Virol., April 15, 2007; 81(8): 4357 - 4362. [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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