{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,2]],"date-time":"2026-03-02T03:25:17Z","timestamp":1772421917919,"version":"3.50.1"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2229,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: RDP3 is a new version of the RDP program for characterizing recombination events in DNA-sequence alignments. Among other novelties, this version includes four new recombination analysis methods (3SEQ, VISRD, PHYLRO and LDHAT), new tests for recombination hot-spots, a range of matrix methods for visualizing over-all patterns of recombination within datasets and recombination-aware ancestral sequence reconstruction. Complementary to a high degree of analysis flow automation, RDP3 also has a highly interactive and detailed graphical user interface that enables more focused hands-on cross-checking of results with a wide variety of newly implemented phylogenetic tree construction and matrix-based recombination signal visualization methods. The new RDP3 can accommodate large datasets and is capable of analyzing alignments ranging in size from 1000\u00d710 kilobase sequences to 20\u00d72 megabase sequences within 48 h on a desktop PC.<\/jats:p>\n               <jats:p>Availability: RDP3 is available for free from its web site http:\/\/darwin.uvigo.es\/rdp\/rdp.html<\/jats:p>\n               <jats:p>Contact: \u00a0darrenpatrickmartin@gmail.com<\/jats:p>\n               <jats:p>Supplementary information: The RDP3 program manual contains detailed descriptions of the various methods it implements and a step-by-step guide describing how best to use these.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq467","type":"journal-article","created":{"date-parts":[[2010,8,27]],"date-time":"2010-08-27T01:14:52Z","timestamp":1282871692000},"page":"2462-2463","source":"Crossref","is-referenced-by-count":1450,"title":["RDP3: a flexible and fast computer program for analyzing recombination"],"prefix":"10.1093","volume":"26","author":[{"given":"Darren P.","family":"Martin","sequence":"first","affiliation":[{"name":"1 Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, 2Centre for High Performance Computing, Rosebank, Cape Town, South Africa, 3Department of Microbiology and Immunology, Rega Institute, K.U. Leuven, Belgium, 4School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK, 5Department of Biochemistry, Genetics and Immunology, University of Vigo, Spain and 6CIRAD, UMR 53 PVBMT CIRAD-Universit\u00e9 de la R\u00e9union, P\u00f4le de Protection des Plantes, Ligne Paradis, La R\u00e9union"},{"name":"1 Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, 2Centre for High Performance Computing, Rosebank, Cape Town, South Africa, 3Department of Microbiology and Immunology, Rega Institute, K.U. Leuven, Belgium, 4School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK, 5Department of Biochemistry, Genetics and Immunology, University of Vigo, Spain and 6CIRAD, UMR 53 PVBMT CIRAD-Universit\u00e9 de la R\u00e9union, P\u00f4le de Protection des Plantes, Ligne Paradis, La R\u00e9union"}]},{"given":"Philippe","family":"Lemey","sequence":"additional","affiliation":[{"name":"1 Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, 2Centre for High Performance Computing, Rosebank, Cape Town, South Africa, 3Department of Microbiology and Immunology, Rega Institute, K.U. Leuven, Belgium, 4School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK, 5Department of Biochemistry, Genetics and Immunology, University of Vigo, Spain and 6CIRAD, UMR 53 PVBMT CIRAD-Universit\u00e9 de la R\u00e9union, P\u00f4le de Protection des Plantes, Ligne Paradis, La R\u00e9union"}]},{"given":"Martin","family":"Lott","sequence":"additional","affiliation":[{"name":"1 Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, 2Centre for High Performance Computing, Rosebank, Cape Town, South Africa, 3Department of Microbiology and Immunology, Rega Institute, K.U. Leuven, Belgium, 4School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK, 5Department of Biochemistry, Genetics and Immunology, University of Vigo, Spain and 6CIRAD, UMR 53 PVBMT CIRAD-Universit\u00e9 de la R\u00e9union, P\u00f4le de Protection des Plantes, Ligne Paradis, La R\u00e9union"},{"name":"1 Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, 2Centre for High Performance Computing, Rosebank, Cape Town, South Africa, 3Department of Microbiology and Immunology, Rega Institute, K.U. Leuven, Belgium, 4School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK, 5Department of Biochemistry, Genetics and Immunology, University of Vigo, Spain and 6CIRAD, UMR 53 PVBMT CIRAD-Universit\u00e9 de la R\u00e9union, P\u00f4le de Protection des Plantes, Ligne Paradis, La R\u00e9union"},{"name":"1 Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, 2Centre for High Performance Computing, Rosebank, Cape Town, South Africa, 3Department of Microbiology and Immunology, Rega Institute, K.U. Leuven, Belgium, 4School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK, 5Department of Biochemistry, Genetics and Immunology, University of Vigo, Spain and 6CIRAD, UMR 53 PVBMT CIRAD-Universit\u00e9 de la R\u00e9union, P\u00f4le de Protection des Plantes, Ligne Paradis, La R\u00e9union"}]},{"given":"Vincent","family":"Moulton","sequence":"additional","affiliation":[{"name":"1 Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, 2Centre for High Performance Computing, Rosebank, Cape Town, South Africa, 3Department of Microbiology and Immunology, Rega Institute, K.U. Leuven, Belgium, 4School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK, 5Department of Biochemistry, Genetics and Immunology, University of Vigo, Spain and 6CIRAD, UMR 53 PVBMT CIRAD-Universit\u00e9 de la R\u00e9union, P\u00f4le de Protection des Plantes, Ligne Paradis, La R\u00e9union"}]},{"given":"David","family":"Posada","sequence":"additional","affiliation":[{"name":"1 Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, 2Centre for High Performance Computing, Rosebank, Cape Town, South Africa, 3Department of Microbiology and Immunology, Rega Institute, K.U. Leuven, Belgium, 4School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK, 5Department of Biochemistry, Genetics and Immunology, University of Vigo, Spain and 6CIRAD, UMR 53 PVBMT CIRAD-Universit\u00e9 de la R\u00e9union, P\u00f4le de Protection des Plantes, Ligne Paradis, La R\u00e9union"}]},{"given":"Pierre","family":"Lefeuvre","sequence":"additional","affiliation":[{"name":"1 Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, 2Centre for High Performance Computing, Rosebank, Cape Town, South Africa, 3Department of Microbiology and Immunology, Rega Institute, K.U. Leuven, Belgium, 4School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK, 5Department of Biochemistry, Genetics and Immunology, University of Vigo, Spain and 6CIRAD, UMR 53 PVBMT CIRAD-Universit\u00e9 de la R\u00e9union, P\u00f4le de Protection des Plantes, Ligne Paradis, La R\u00e9union"},{"name":"1 Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, 2Centre for High Performance Computing, Rosebank, Cape Town, South Africa, 3Department of Microbiology and Immunology, Rega Institute, K.U. Leuven, Belgium, 4School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK, 5Department of Biochemistry, Genetics and Immunology, University of Vigo, Spain and 6CIRAD, UMR 53 PVBMT CIRAD-Universit\u00e9 de la R\u00e9union, P\u00f4le de Protection des Plantes, Ligne Paradis, La R\u00e9union"}]}],"member":"286","published-online":{"date-parts":[[2010,8,26]]},"reference":[{"key":"2023012508165959100_B1","doi-asserted-by":"crossref","first-page":"1133","DOI":"10.1534\/genetics.109.113423","article-title":"The effect of recombination on the reconstruction of ancestral sequences","volume":"184","author":"Arenas","year":"2010","journal-title":"Genetics"},{"key":"2023012508165959100_B2","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/1471-2148-6-15","article-title":"Phylogenetic identification of lateral genetic transfer events","volume":"6","author":"Beiko","year":"2006","journal-title":"BMC Evol. Biol."},{"key":"2023012508165959100_B3","doi-asserted-by":"crossref","first-page":"1035","DOI":"10.1534\/genetics.106.068874","article-title":"An exact nonparametric method for inferring mosaic structure in sequence triplets","volume":"176","author":"Boni","year":"2007","journal-title":"Genetics"},{"key":"2023012508165959100_B4","doi-asserted-by":"crossref","first-page":"3497","DOI":"10.1093\/nar\/gkg500","article-title":"Multiple sequence alignment with the Clustal series of programs","volume":"31","author":"Chenna","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012508165959100_B5","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1093\/bioinformatics\/16.7.573","article-title":"Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences","volume":"16","author":"Gibbs","year":"2000","journal-title":"Bioinformatics"},{"key":"2023012508165959100_B6","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1080\/10635150390235520","article-title":"A. simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood","volume":"52","author":"Guindon","year":"2003","journal-title":"Syst. Biol."},{"key":"2023012508165959100_B7","doi-asserted-by":"crossref","first-page":"11827","DOI":"10.1128\/JVI.01100-06","article-title":"Recombination patterns in aphthoviruses mirror those found in other picornaviruses","volume":"80","author":"Heath","year":"2006","journal-title":"J. Virol."},{"key":"2023012508165959100_B8","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1093\/oxfordjournals.molbev.a026121","article-title":"Phylogenetic evidence for recombination in dengue virus","volume":"16","author":"Holmes","year":"1999","journal-title":"Mol. Biol. Evol."},{"key":"2023012508165959100_B9","first-page":"291","article-title":"A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences","volume":"12","author":"Jakobsen","year":"1996","journal-title":"Comput. Appl. Biosci."},{"key":"2023012508165959100_B10","doi-asserted-by":"crossref","first-page":"e1000581","DOI":"10.1371\/journal.pcbi.1000581","article-title":"An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1","volume":"5","author":"Kosakovsky","year":"2009","journal-title":"PLoS Comput. Biol."},{"key":"2023012508165959100_B11","doi-asserted-by":"crossref","first-page":"e181","DOI":"10.1371\/journal.ppat.0030181","article-title":"Avoidance of protein fold disruption in natural virus recombinants","volume":"3","author":"Lefeuvre","year":"2007","journal-title":"PLoS Pathog."},{"key":"2023012508165959100_B12","doi-asserted-by":"crossref","first-page":"2697","DOI":"10.1128\/JVI.02152-08","article-title":"Widely conserved recombination patterns among single-stranded DNA viruses","volume":"83","author":"Lefeuvre","year":"2009","journal-title":"J. Virol."},{"key":"2023012508165959100_B13","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1186\/1471-2105-10-126","article-title":"Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning","volume":"10","author":"Lemey","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023012508165959100_B14","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1128\/JVI.73.1.152-160.1999","article-title":"Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination","volume":"73","author":"Lole","year":"1999","journal-title":"J. Virol."},{"key":"2023012508165959100_B15","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1093\/bioinformatics\/bth490","article-title":"RDP2: recombination detection and analysis from sequence alignments","volume":"21","author":"Martin","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012508165959100_B16","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1089\/aid.2005.21.98","article-title":"A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints","volume":"21","author":"Martin","year":"2005","journal-title":"AIDS Res. Hum. Retrovir."},{"key":"2023012508165959100_B17","first-page":"126","article-title":"Analyzing the mosaic structure of genes","volume":"34","author":"Maynard Smith","year":"1992","journal-title":"J. Mol. Evol."},{"key":"2023012508165959100_B18","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1126\/science.1092500","article-title":"The fine-scale structure of recombination rate variation in the human genome","volume":"304","author":"McVean","year":"2004","journal-title":"Science"},{"key":"2023012508165959100_B19","doi-asserted-by":"crossref","first-page":"3034","DOI":"10.1093\/bioinformatics\/bti459","article-title":"Dual multiple change-point model leads to more accurate recombination detection","volume":"21","author":"Minin","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012508165959100_B20","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1006\/viro.1999.0056","article-title":"Possible emergence of new geminiviruses by frequent recombination","volume":"265","author":"Padidam","year":"1999","journal-title":"Virology"},{"key":"2023012508165959100_B21","doi-asserted-by":"crossref","first-page":"13757","DOI":"10.1073\/pnas.241370698","article-title":"Evaluation of methods for detecting recombination from DNA sequences: computer simulations","volume":"98","author":"Posada","year":"2001","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012508165959100_B22","doi-asserted-by":"crossref","first-page":"1572","DOI":"10.1093\/bioinformatics\/btg180","article-title":"MrBayes 3: Bayesian phylogenetic inference under mixed models","volume":"19","author":"Ronquist","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012508165959100_B23","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1186\/1471-2105-7-265","article-title":"A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes","volume":"7","author":"Schultz","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023012508165959100_B24","first-page":"553","article-title":"Protein building blocks preserved by recombination","volume":"9","author":"Voigt","year":"2002","journal-title":"Nat. Struct. Biol."},{"key":"2023012508165959100_B25","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1093\/oxfordjournals.molbev.a025929","article-title":"Phylogenetic profiles: a graphical method for detecting genetic recombinations in homologous sequences","volume":"15","author":"Weiller","year":"1998","journal-title":"Mol. Biol. Evol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/19\/2462\/48854853\/bioinformatics_26_19_2462.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/19\/2462\/48854853\/bioinformatics_26_19_2462.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T08:17:39Z","timestamp":1674634659000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/19\/2462\/230344"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,8,26]]},"references-count":25,"journal-issue":{"issue":"19","published-print":{"date-parts":[[2010,10,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq467","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,10,1]]},"published":{"date-parts":[[2010,8,26]]}}}