Recombination Detection and Analysis Using RDP3
- Darren P. Martin
- … show all 1 hide
Purchase on Springer.com
$49.95 / €39.95 / £34.95*
* Final gross prices may vary according to local VAT.
Recombination between nucleotide sequences is a major process influencing the evolution of most species on Earth. While its evolutionary value is a matter of quite intense debate, so too is the influence of recombination on evolutionary analysis methods that assume nucleotide sequences replicate without recombining. The crux of the problem is that when nucleic acids recombine, the daughter or recombinant molecules no longer have a single evolutionary history. All analysis methods that derive increased power from correctly inferring evolutionary relationships between sequences will therefore be at least mildly sensitive to the effects of recombination. The importance of considering recombination in evolutionary studies is underlined by the bewildering array of currently available methods and software tools for analysing and characterising it in various classes of nucleotide sequence datasets. Here we will examine the use of some of these tools to derive and test recombination hypotheses for datasets containing a moderate degree of nucleotide sequence diversity.
- Martin, D. P., Williamson, C., and Posada, D. (2005) RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 21, 260–2. CrossRef
- Martin, D., and Rybicki, E. (2000) RDP: detection of recombination amongst aligned sequences. Bioinformatics 16, 562–3. CrossRef
- Padidam, M., Sawyer, S., and Fauquet, C. M. (1999) Possible emergence of new geminiviruses by frequent recombination. Virology 265, 218–25. CrossRef
- Maynard-Smith, J. (1992) Analyzing the mosaic structure of genes. J Mol Evol 34, 126–9.
- Posada, D., and Crandall, K. A. (2001) Evaluation of methods for detecting recombination from DNA sequences: Computer simulations. Proc Natl Acad Sci USA 98, 13757–62. CrossRef
- Martin, D. P., Posada, D., Crandall, K. A., and Williamson, C. (2005) A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Res Hum Retroviruses 21, 98–102. CrossRef
- Boni M. F., Posada, D., and Feldman, M. W. (2007) An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics 176, 1035–47. CrossRef
- Gibbs, M. J., Armstrong, J. S., and Gibbs, A. J. (2000) Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 16, 573–82. CrossRef
- Holmes, E. C., Worobey, M., and Rambaut, A. (1999) Phylogenetic evidence for recombination in dengue virus. Mol Biol Evol 16, 405–9.
- Felsenstein, J. (1989) PHYLIP – Phylogeny Inference Package (Version 3.2). Cladistics 5, 164–6.
- Guindon, S., and Gascuel, O. (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52, 696–704. CrossRef
- Weiller, G. F. (1998) Phylogenetic profiles: a graphical method for detecting genetic recombinations in homologous sequences. Mol Biol Evol 15, 326–35.
- McGuire, G., and Wright, F. (2000) TOPAL 2.0: improved detection of mosaic sequences within multiple alignments. Bioinformatics 16, 130–4. CrossRef
- Recombination Detection and Analysis Using RDP3
- Book Title
- Bioinformatics for DNA Sequence Analysis
- pp 185-205
- Print ISBN
- Online ISBN
- Series Title
- Methods in Molecular Biology
- Series Volume
- Series Subtitle
- Methods and Protocols
- Series ISSN
- Humana Press
- Copyright Holder
- Humana Press
- Additional Links
- gene conversion
- phylogenetic trees
- Industry Sectors
To view the rest of this content please follow the download PDF link above.