Recombination Detection Program (RDP)

RDP (Recombination detection program) is software that applies a number of recombination detection and analysis algorithms. It runs under Windows 95/98/NT/XP. You may download:

• the full program (smaller download) (RDP3 Beta 41 including VB runtimes, accesory apps & LDHat lookup tables)
• the full program (bigger download) (RDP3 Beta 41 including VB runtimes, accesory apps, LDHat lookup tables and a large 3Seq p-value lookup table)
• a (still very out of date) user manual
• an old version, RDP2, that can be used to load and explore older project files (RDP2 and earlier)

Note that if you experience a program crash when trying to change analysis settings try changing your Windows language setting to English and rerunning the program. I'm busy trying to fix a very elusive bug that crashes the program if it receives decimal numbers with a comma rather than a point used as a decimal separator.

If you are a VISTA user you may need to give RDP3 administrator rights for it to run properly. You do this by copying a shortcut to the program onto your desktop, right clicking on the shortcut icon, selecting the 'options' menu item, and then selecting the 'compatibility' tab. One of the options offered on this tab is to allow RDP3 abministrator rights.

Please cite either:

Heath, L., van der Walt, E., Varsani, A. & Martin D.P. (2006). Recombination patterns in aphthoviruses mirror those found in other picornaviruses. J Virol 80, 11827-11832.

or

Martin, D. P., Williamson, C. & Posada, D. (2005). RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 21, 260-262.

Also, if you use any of the following features in RDP3 please cite the appropriate papers

• The RDP method: Martin, D. & Rybicki, E. (2000). RDP: detection of recombination amongst aligned sequences. Bioinformatics 16, 562-563.
• The GENECONV method: Padidam, M., Sawyer, S. & Fauquet, C. M. (1999). Possible emergence of new geminiviruses by frequent recombination. Virology 265, 218-225.
• The Bootscan/Recscan method: Martin, D. P., Posada, D., Crandall, K. A. & Williamson, C. (2005). A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Res Hum Retroviruses 21, 98-102.
• The MaxChi method: Maynard Smith, J. (1992). Analyzing the mosaic structure of genes. J Mol Evol 34, 126-129.
• The Chimaera method: Posada, D. & Crandall, K. A. (2001). Evaluation of methods for detecting recombination from DNA sequences: Computer simulations. Proc Natl Acad Sci 98, 13757-13762.
• The SiScan method: Gibbs, M. J., Armstrong, J. S. & Gibbs, A. J. (2000). Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 16, 573-582.
• The 3Seq method: Boni M.F., Posada, D. & Feldman, M.W. (2007). An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics 176, 1035-1047.
• The LARD method: Holmes E.C., Worobey, M. & Rambaut,A. (1999). Phylogenetic evidence for recombination in dengue virus. Mol Biol and Evol 16, 405-409.
• The Topal/DSS method: McGuire, G. & Wright,F. (2000). TOPAL 2.0: Improved detection of mosaic sequences within multiple alignments. Bioinformatics 16, 130-134.
• The Phylpro method: Weiller, G.F. (1998). Phylogenetic profiles: a graphical method for detecting genetic recombinations in homologous sequences. Mol Biol Evol 15, 326-335.
• The VisRD methods: Lemey, P., Lott, M., Martin, D.P. & Moulton, V. (2009). Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning. BMC Bioinformatics 10, 126.
• Recombination count matrices: Lefeuvre, P., Lett, J.M., Reynaud, B., Martin, D.P. (2007). Avoidance of protein fold disruption in natural virus recombinants. PLoS Pathog 11:e181.
• Recombination hotspot test: Heath, L., van der Walt, E., Varsani, A. & Martin D.P. (2006). Recombination patterns in aphthoviruses mirror those found in other picornaviruses. J Virol 80, 11827-11832.
• Recombination rate plots: McVean, G. A. T., Myers, S. R., Hunt, S., Deloukas, P., Bentley, D. R. & Donnelly, P. (2004). The Fine-Scale Structure of Recombination Rate Variation in the Human Genome. Science 304, 581-584.
• RMin/LD matrices: McVean, G., Awadalla, P. & Fearnhead, P. (2002). A Coalescent-Based Method for Detecting and Estimating Recombination From Gene Sequences. Genetics 160, 1231-1241.
• Neighbor joining or least squares trees: Felsenstein, J. (1989). PHYLIP – Phylogeny inference package (version 3.2). Cladistics 5, 164–166.
• Maximum likelihood trees: Guindon, S. & Gascuel, O. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52, 696-704.
• Bayesian trees: Ronquist, F. & Huelsenbeck, J.P. (2003). MRBAYES 3:Bayesian phylogenetic inference under mixed models. Bioinformatics 19,1572-1574.

To be informed about bugs or updates email Darren Martin.

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