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{"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
transitons and transversions.}
\item{``logdet''}{The Log-Det distance, developed by Lockhart et
- al. (1994), is related to BH87. However, this distance is symmetric.}
+ al. (1994), is related to BH87. However, this distance is
+ symmetric. Formulae from Gu and Li (1996) are used.
+ \code{dist.logdet} in \pkg{phangorn} uses a different
+ implementation that gives substantially different distances for
+ low-diverging sequences.}
\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
sequences of unequal base compositions. \emph{Proceedings of the
National Academy of Sciences USA}, \bold{92}, 11317--11321.
+ Gu, X. and Li, W.-H. (1996) Bias-corrected paralinear and LogDet
+ distances and tests of molecular clocks and phylogenies under
+ nonstationary nucleotide frequencies. \emph{Molecular Biology and
+ Evolution}, \bold{13}, 1375--1383.
+
Jukes, T. H. and Cantor, C. R. (1969) Evolution of protein
molecules. in \emph{Mammalian Protein Metabolism}, ed. Munro, H. N.,
pp. 21--132, New York: Academic Press.
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}},