RDP3: a flexible and fast computer program for analyzing recombination

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ID: 291716
2010
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Abstract
Abstract 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.
Reference Key
openalex_W2141008678 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Darren P. Martin, Philippe Lemey, Martin Lott, Vincent Moulton, David Posada, Pierre Lefeuvre
Journal BMC Bioinformatics
Year 2010
DOI
10.1093/bioinformatics/btq467
URL
https://doi.org/10.1093/bioinformatics/btq467
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