RDP3: a flexible and fast computer program for analyzing recombination

By Darren P. Martin, Philippe Lemey, M. Lott, Vincent Moulton, David Posada, P. Lefeuvre. Bioinform., 2010

1,703 citations recorded by the source corpus.

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 1000×10 kilobase sequences to 20×2 megabase sequences within 48 h on a desktop PC. Availability: RDP3 is available for free from its web site http://darwin.uvigo.es/rdp/rdp.html Contact: darrenpatrickmartin@gmail.com 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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/3432d67b351a7c615cee15451f3e646f45eb91c5

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In Molecular Biology

Citations in the corpus

Molecular Evolution of Zika Virus during Its Emergence in the 20th Century (2014, methodology): “01 that were confirmed by four or more methods were considered, using the Bonferroni correction to prevent false positive results [39], as implemented in the RDP program [31].”
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins (2014, methodology): “More recent algorithms of this type, such as RDP3 (13), cBrother (14) and GARD (15), are able to identify the breakpoints in putative recombinant sequences based on the relative divergence between multiple representatives of a population in different regions of a sequence alignment.”