dnds {ape} | R Documentation |
This function computes the pairwise ratios dN/dS for a set of aligned DNA sequences using Li's (1993) method.
dnds(x, code = 1, codonstart = 1, quiet = FALSE)
x |
an object of class |
code |
an integer value giving the genetic code to be used. Currently only 1 (standard code) and 2 (vertebrate mitochondrial code) are supported. |
codonstart |
an integer giving where to start the translation. This should be 1, 2, or 3, but larger values are accepted and have for effect to start the translation further within the sequence. |
quiet |
single logical value: whether to indicate progress of calculations. |
an object of class "dist"
.
Emmanuel Paradis
Li, W.-H. (1993) Unbiased estimation of the rates of synonymous and nonsynonymous substitution. Journal of Molecular Evolution, 36, 96–99.
data(woodmouse) res <- dnds(woodmouse, quiet = TRUE) # NOT correct res2 <- dnds(woodmouse, code = 2, quiet = TRUE) # using the correct code identical(res, res2)