This function computes the pairwise ratios dN/dS for a set of aligned
DNA sequences using Li's (1993) method.
Usage
dnds(x, code = 1, codonstart = 1, quiet = FALSE)
Arguments
x
an object of class "DNAbin" (matrix or list) with the
aligned sequences.
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.
Value
an object of class "dist".
References
Li, W.-H. (1993) Unbiased estimation of the rates of synonymous and
nonsynonymous substitution. Journal of Molecular Evolution,
36, 96--99.
# NOT RUN {data(woodmouse)
res <- dnds(woodmouse, quiet = TRUE) # NOT correctres2 <- dnds(woodmouse, code = 2, quiet = TRUE) # using the correct codeidentical(res, res2)
# }