TOPAL 2.0: improved detection of mosaic sequences within multiple alignments.
BACKGROUND
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.


RESULTS
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.


BACKGROUND
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.


BACKGROUND
frank@bioss.sari.ac.uk
McGuire
G
G
Isaac Newton Institute for Mathematical Sciences, Cambridge, UK.
Wright
F
F
D000465:Algorithms; D014644:Genetic Variation; D008432:Mathematical Computing; D011995:Recombination, Genetic; D016415:Sequence Alignment / Q000379:methods*; D012984:Software