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Bioinformatics. 2010 Oct 1;26(19):2462-3. doi: 10.1093/bioinformatics/btq467. Epub 2010 Aug 26.

RDP3: a flexible and fast computer program for analyzing recombination.

Author information

1
Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Centre for High Performance Computing, Rosebank, Cape Town, South Africa. darrenpatrickmartin@gmail.com

Abstract

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.

PMID:
20798170
PMCID:
PMC2944210
DOI:
10.1093/bioinformatics/btq467
[Indexed for MEDLINE]
Free PMC Article

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