RDP: detection of recombination amongst aligned sequences

By Darren P. Martin, E. Rybicki. Bioinform., 2000

1,532 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/534cbfc17de6498e113ecb4eb55049231433f1de

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

1. David Posada
2. Hervé Philippe
3. Maciej F. Boni
4. T. C. Bruen
5. David Bryant
6. Michal Feldman
7. Carolyn Williamson
8. Darren P. Martin

In Molecular Biology

1. Hervé Philippe
2. T. C. Bruen
3. David Bryant
4. David Posada
5. Carolyn Williamson
6. Darren P. Martin
7. Maciej F. Boni
8. Michal Feldman

Citations in the corpus

• RDP2: recombination detection and analysis from sequence alignments (2005, methodology): “rdp (RDP method) T V ++ Martin and Rybicki (2000)”
• Molecular Evolution of Human Coronavirus Genomes (2016, neutral): “A common approach is to use different methodologies to identify breakpoint locations and contributing sequences (e.g., RDP [72] ).”
• An Exact Nonparametric Method for Inferring Mosaic Structure in Sequence Triplets (2007, methodology): “Power and false positives: We compared the power and false-positive rates of our D-method to the 14 methods evaluated in Posada and Crandall (2001).”
• RDP4: Detection and analysis of recombination patterns in virus genomes (2015, methodology): “Besides the original RDP method (Martin and Rybicki 2000), these methods include BOOTSCAN (Salminen et al. 1995), MAXCHI (Maynard Smith 1992), CHIMAERA (Posada and Crandall 2001), 3 SEQ (Boni, Posada, and Feldman 2007), GENECONV (Padidam, Sawyer, and Fauquet 1999), LARD (Holmes, Worobey, and…”
• Evaluation of methods for detecting recombination from DNA sequences: empirical data. (2002, methodology): “…100 Monte Carlo replicates were used Default window settings were used (minimum size (cid:53) step (9) Recombination Detection Program (Martin and Rybicki 2000 The Windows program Rdp (Martin and Rybicki 2000) (ftp://ftp.uct.ac.za/pub/data/geminivirus/recomb. htm) was generously…”
• Molecular Evolution of Zika Virus during Its Emergence in the 20th Century (2014, background): “[32], GENECONV [33], Chimaera [34], MaxChi [35], Bootscan [36], SiScan [37] and 3Seq [38] methods to uncover evidence for recombination events.”
• A Simple and Robust Statistical Test for Detecting the Presence of Recombination (2006, methodology): “These studies have established that methods such as Geneconv (Sawyer 1989), Max x(2) (Maynard Smith 1992), RDP (Martin and Rybicki 2000), Phypro (Weiller 1998), RecPars (Hein 1990, 1993), and neighbor similarity score (NSS) ( Jakobsen and Easteal 1996) efficiently detect recombination in a wide rang”