About Site Map Submit Contact Us Log in | Create an account
Create an account Log In
Average Rating
User Rating:
Visitors Rating:
My rating:

Write review
  • License: Freeware
  • Last update: 6 years ago
  • Total downloads: 470
  • Price: Free |
  • Operating system: Win All
  • Publisher: Darren Martin
See full specifications

windows default iconRDP Publisher's description

RDP (Recombination detection program) is software that applies a number of recombination detection and analysis algorithms.

RDP (Recombination detection program) is software that applies a number of recombination detection and analysis algorithms. It runs under Windows 95/98/NT/XP/VISTA/7. You may

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. [PDF]
* 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. [PDF]
* 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. [PDF]
* 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. [PDF]
* 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.

System Requirements:

No special requirements.
Program Release Status: New Release
Program Install Support: Install and Uninstall

Is RDP your software?

Manage your software

Most Popular

windows default icon PhotoShine 4.51
Add your photo into different beautiful templates
windows default icon Xorax Contact Sheet 1.3
"Xorax Contact Sheet" is a simple tool that generates contact sheet (index file)
windows default icon MapInfo Professional 10.5
MapInfo Professional is a powerful Microsoft Windows–based mapping and geographic analysis application.
windows default icon Circuit Wizard Professional Edition 1.10
Circuit Wizard, our flagship product, is a revolutionary new system that combines circuit design, PCB design,... Read more
windows default icon Photo Makeup Editor 1.85
Photo Makeup Editor is a photo retouching and virtual makeup software.

Related Category

» Animation Tools (180)
» CAD (1449)
» Editors (1260)
» Font Tools (714)
» Icon Tools (153)
» Other (1297)
» Screen Capture (394)
» Viewers (426)