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

1468 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

@article{6b0bfd37026a4a1ba870b6230ddcdfc8,

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.",

author = "Martin, {Darren P.} and Philippe Lemey and Martin Lott and Vincent Moulton and David Posada and Pierre Lefeuvre",

year = "2010",

doi = "10.1093/bioinformatics/btq467",

language = "English",

volume = "26",

pages = "2462--2463",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "19",

}

TY - JOUR

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

AU - Martin, Darren P.

AU - Lemey, Philippe

AU - Lott, Martin

AU - Moulton, Vincent

AU - Posada, David

AU - Lefeuvre, Pierre

PY - 2010

Y1 - 2010

N2 - 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.

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.

U2 - 10.1093/bioinformatics/btq467

DO - 10.1093/bioinformatics/btq467

M3 - Article

VL - 26

SP - 2462

EP - 2463

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 19

ER -