RDP3: a flexible and fast computer program for analyzing recombination

Martin, Darren P., Lemey, Philippe, Lott, Martin, Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435, Posada, David and Lefeuvre, Pierre (2010) RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics, 26 (19). pp. 2462-2463. ISSN 1367-4803

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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.

Item Type: Article
Faculty \ School: Faculty of Science > School of Computing Sciences
Depositing User: Users 2731 not found.
Date Deposited: 18 Oct 2011 13:48
Last Modified: 23 Oct 2022 01:33
URI: https://ueaeprints.uea.ac.uk/id/eprint/35051
DOI: 10.1093/bioinformatics/btq467

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