\arguments{
\item{x}{a matrix or a list containing the DNA sequences.}
\item{model}{a character string specifying the evlutionary model to be
- used; must be one of \code{"raw"}, \code{"JC69"}, \code{"K80"} (the
- default), \code{"F81"}, \code{"K81"}, \code{"F84"}, \code{"BH87"},
- \code{"T92"}, \code{"TN93"}, \code{"GG95"}, \code{"logdet"}, or
- \code{"paralin"}.}
+ used; must be one of \code{"raw"}, \code{"N"}, \code{"JC69"},
+ \code{"K80"} (the default), \code{"F81"}, \code{"K81"},
+ \code{"F84"}, \code{"BH87"}, \code{"T92"}, \code{"TN93"},
+ \code{"GG95"}, \code{"logdet"}, or \code{"paralin"}.}
\item{variance}{a logical indicating whether to compute the variances
of the distances; defaults to \code{FALSE} so the variances are not
computed.}
brief description is given below; more details can be found in the
References.
- \item{``raw''}{This is simply the proportion of sites that differ
- between each pair of sequences. This may be useful to draw
- ``saturation plots''. The options \code{variance} and \code{gamma}
- have no effect, but \code{pairwise.deletion} can.}
+\itemize{
+ \item{``raw'', ``N''}{This is simply the proportion or the number of
+ sites that differ between each pair of sequences. This may be useful
+ to draw ``saturation plots''. The options \code{variance} and
+ \code{gamma} have no effect, but \code{pairwise.deletion} can.}
\item{``JC69''}{This model was developed by Jukes and Cantor (1969). It
assumes that all substitutions (i.e. a change of a base by another
\item{``paralin''}{Lake (1994) developed the paralinear distance which
can be viewed as another variant of the Barry--Hartigan distance.}
-}
+}}
\value{
an object of class \link[stats]{dist} (by default), or a numeric
matrix if \code{as.matrix = TRUE}. If \code{model = "BH87"}, a numeric