RDP2: recombination detection and analysis from sequence alignments

Martin, D. P.
Williamson, C.
Posada, D.

¹Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, 7000, South Africa
²Department of Biochemistry, Genetics and Immunology, University of Vigo, 36200 Vigo, Spain

Received on April 20, 2004; revised on June 28, 2004; accepted on August 13, 2004; Advance Access publication September 17, 2004

^*To whom correspondence should be addressed.

Availability: RDP2 is available free from the RDP2 website (http://darwin.uvigo.es/rdp/rdp.html)

Contact: [email protected]

Supplementary information: Detailed descriptions of RDP2 and the methods it implements are included in the program manual, which can be downloaded from the RDP2 website.

Bioinformatics 21(2):p 260-262, January 15, 2005.

RDP2 is a Windows 95/XP program that examines nucleotide sequence alignments and attempts to identify recombinant sequences and recombination breakpoints using 10 published recombination detection methods, including GENECONV, BOOTSCAN, MAXIMUM χ², CHIMAERA and SISTER SCANNING. The program enables fast automated analysis of large alignments (up to 300 sequences containing 13 000 sites), and interactive exploration, management and verification of results with different recombination detection and tree drawing methods.