-}
-\description{
- This function computes the relative frequencies (i.e. percentages) of
- the four DNA bases (adenine, cytosine, guanine, and thymidine) from a
- sample of sequences.
+ \item{y}{a vector with a single DNA sequence.}
+ \item{freq}{a logical specifying whether to return the proportions
+ (the default) or the absolute frequencies (counts).}
+ \item{all}{a logical; by default only the counts of A, C, G, and T are
+ returned. If \code{all = TRUE}, all counts of bases, ambiguous codes,
+ missing data, and alignment gaps are returned.}