RDP3: a flexible and fast computer program for analyzing recombination

RDP3: a flexible and fast computer program for analyzing recombination 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 100010 kilobase sequences to 202 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.htmlContact: darrenpatrickmartin@gmail.comSupplementary 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. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Bioinformatics Oxford University Press

RDP3: a flexible and fast computer program for analyzing recombination

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Publisher
Oxford University Press
Copyright
© Published by Oxford University Press.
ISSN
1367-4803
eISSN
1460-2059
D.O.I.
10.1093/bioinformatics/btq467
Publisher site
See Article on Publisher Site

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 100010 kilobase sequences to 202 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.htmlContact: darrenpatrickmartin@gmail.comSupplementary 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.

Journal

BioinformaticsOxford University Press

Published: Oct 1, 2010

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