base.freq = NULL, as.matrix = FALSE)
}
\arguments{
- \item{x}{a matrix or a list containing the DNA sequences.}
+ \item{x}{a matrix or a list containing the DNA sequences; this must be
+ of class \code{"DNAbin"} (use \code{\link{as.DNAbin}} is they are
+ stored as character).}
\item{model}{a character string specifying the evlutionary model to be
used; must be one of \code{"raw"}, \code{"N"}, \code{"JC69"},
\code{"K80"} (the default), \code{"F81"}, \code{"K81"},
brief description is given below; more details can be found in the
References.
+\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
\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
substitutions in the control region of mitochondrial DNA in humans and
chimpanzees. \emph{Molecular Biology and Evolution}, \bold{10}, 512--526.
}
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
+\author{Emmanuel Paradis}
\seealso{
\code{\link{read.GenBank}}, \code{\link{read.dna}},
\code{\link{write.dna}}, \code{\link{DNAbin}},