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RDP3: a flexible and fast computer program for analyzing recombination
Open accessAbstract
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.
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Metadata
- Authors
- Martin, D. P., Lemey, P., Lott, M., Moulton, V., Posada, D., & Lefeuvre, P.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-08-26
- Volume
- 26
- Issue
- 19
- Pages
- 2462-2463
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2141008678
- Cited by
- 1,613
- References
- 0
- FWCI
- 63.33
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Martin, D. P., Lemey, P., Lott, M., Moulton, V., Posada, D., & Lefeuvre, P. (2010). RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics. https://doi.org/10.1093/bioinformatics/btq467
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