SLR (Sitewise Likehood Ratio) is a program to detect sites in coding DNA that are unusually conserved and/or unusually variable (that is, evolving under purify or positive selection) by analysing the pattern of changes for an alignment of sequences on an evolutionary tree. The strength of selection at each site is determined by comparing the rate of nonsynonymous (amino acid changing) substitutions to that of synonymous (silent) substituions, the latter assumed to be invisible to selection and so evolving in a strictly neutral fashion.
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Genetics. 2005 Mar;169(3):1753-62. Epub 2005 Jan 16.
Detecting amino acid sites under positive selection and purifying selection.
Massingham T, Goldman N.