Comparisons of Site- and Haplotype-Frequency Methods for Detecting Positive Selection
نویسندگان
چکیده
منابع مشابه
In defense of statistical methods for detecting positive selection.
In a highly publicized article, Nozawa et al. (1) claimed that the branch-site model (BSM) (2, 3) was unreliable because it produced excessive false positives in their simulation experiment. BSM uses a likelihood ratio test to detect positive selection that affects particular branches and codons in proteincoding genes, indicated by accelerated nonsynonymous substitution rates. The authors’ conc...
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The branch-site model is a widely popular approach that accommodates for the lineage- and the site-specific heterogeneity of natural selection regimes among coding sequences. This model relies on prior knowledge of the (foreground) lineage(s) evolving under positive selection at some sites. Unfortunately, such prior information is not always available in practice. A more recent technique (Guind...
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Reliabilities of identifying positive selection by the branch-site and the site-prediction methods.
Natural selection operating in protein-coding genes is often studied by examining the ratio (omega) of the rates of nonsynonymous to synonymous nucleotide substitution. The branch-site method (BSM) based on a likelihood ratio test is one of such tests to detect positive selection for a predetermined branch of a phylogenetic tree. However, because the number of nucleotide substitutions involved ...
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ژورنال
عنوان ژورنال: Molecular Biology and Evolution
سال: 2007
ISSN: 0737-4038,1537-1719
DOI: 10.1093/molbev/msm078