TOPAL 2.0: improved detection of mosaic sequences within multiple alignments.
basic_science · Level V
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Abstract
The Dss statistic was proposed by McGuire et al. (Mol. Biol. Evol., 14, 1125-1131, 1997) for scanning data sets for the presence of recombination, an important step in some phylogenetic analyses. The statistic, however, could not distinguish well between among-site rate variation and recombination, and had no statistical test for significant values. This paper addresses these shortfalls. A modification to the Dss statistic is proposed which accounts for rate variation to a large extent. A statistical test, based on parametric bootstrapping, is also suggested. The TOPAL package (version 2) may be accessed from http:/ /www.bioss.sari.ac.uk/frank/Genetics and by anonymous ftp from typ://ftp.bioss.sari.ac.uk in the directory pub/phylogeny/topal. frank@bioss.sari.ac.uk
Medical subject headings
- Genetic Variation
- Recombination, Genetic
- Sequence Alignment
- Software