RDP3: a flexible and fast computer program for analyzing recombination

Darren P. Martin; Philippe Lemey; Martin Lott; Vincent Moulton; David Posada; Pierre Lefeuvre

doi:10.1093/bioinformatics/btq467

RDP3: a flexible and fast computer program for analyzing recombination

Darren P. Martin
, Philippe Lemey
, Martin Lott
, Vincent Moulton
, David Posada
, Pierre Lefeuvre

Research output: Contribution to journal › Article › peer-review

1486 Citations (Scopus)

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.

Original language	English
Pages (from-to)	2462-2463
Number of pages	2
Journal	Bioinformatics
Volume	26
Issue number	19
DOIs	https://doi.org/10.1093/bioinformatics/btq467
Publication status	Published - 2010

Access to Document

10.1093/bioinformatics/btq467

Cite this

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title = "RDP3: a flexible and fast computer program for analyzing recombination",

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.",

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T1 - RDP3: a flexible and fast computer program for analyzing recombination

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AU - Lemey, Philippe

AU - Lott, Martin

AU - Moulton, Vincent

AU - Posada, David

AU - Lefeuvre, Pierre

PY - 2010

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AB - 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.

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