RDP2: recombination detection and analysis from sequence alignments

By Darren P. Martin, Carolyn Williamson, David Posada. Bioinform., 2005

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View Paper: https://www.semanticscholar.org/paper/9c01a48f788695647db19f7f253bf9526b019f61

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Citations in the corpus

Distinguishing importation from diversification of quinolone-resistant Neisseria gonorrhoeae by molecular evolutionary analysis (2007, methodology): “Martin DP, Williamson C, Posada D: RDP2: recombination detection and analysis from sequence alignments.”
Genome Microevolution of Chikungunya Viruses Causing the Indian Ocean Outbreak (2006, methodology): “RDP2 [19] was used to detect putative mosaic sequences.”
Molecular identification of three distinct Polerovirus species and a recombinant Cucurbit aphid-borne yellows virus strain infecting cucurbit crops in Taiwan (2010, methodology): “, 1999), RDP-V2 Beta08 [Recombination Detection Program] (Martin et al., 2005) and the DATAMONKEY webserver for genetic algorithm recombination detection (GARD) and single breaking point (SBP) analysis (Pond & Frost, 2005) were used.”
Ancient Origin and Gene Mosaicism of the Progenitor of Mycobacterium tuberculosis (2005, methodology): “The program RDP version 2 [ 43 ] was used to detect mosaic sequences using the Sawyer’s and chi-square methods.”
Multilocus Sequence Typing System for the Endosymbiont Wolbachia pipientis (2006, methodology): “Ka/Ks Recombination (MaxChi, P 0.01)c gatB ABDF 26 28.7 0.078 37.2 0.093 Yes (G. firmus)d A 13 9.2 0.027 37.8 0.151 No B 11 11.1 0.022 36.6 0.135 No coxA ABDF 27 28.4 0.083 39.3 0.078 No A 11 4.5 0.015 39.9 0.099 No B 14 17.4 0.053 38.7 0.072 Yes (P. sialia [B1], T. confusum, E. formosa) hcpA ABDF 3”
Short Communication Comparative analysis reveals frequent recombination in the parvoviruses (2007, methodology): “To screen for recombination we employed two preliminary detection programs: RDP2 (Martin et al., 2005) and Genetic Algorithms for Recombination Detection (GARD; Kosakovsky Pond et al., 2006).”
Characterization of Pseudomonas syringae pv. actinidiae (Psa) isolated from France and assignment of Psa biovar 4 to a de novo pathovar: Pseudomonas syringae pv. actinidifoliorum pv. nov. (2015, methodology): “Estimations of recombination events were performed using a method based on seven different nonparametric detection algorithms implemented in RDP v. 3.38 (Martin et al., 2005).”