\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
+ \item{model}{a character string specifying the evolutionary model to be
used; must be one of \code{"raw"}, \code{"N"}, \code{"TS"},
\code{"TV"}, \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"}.}
+ \code{"T92"}, \code{"TN93"}, \code{"GG95"}, \code{"logdet"},
+ \code{"paralin"}, \code{"indel"}, or \code{"indelblock"}.}
\item{variance}{a logical indicating whether to compute the variances
of the distances; defaults to \code{FALSE} so the variances are not
computed.}
- \item{gamma}{a value for the gamma parameter which is possibly used to
- apply a gamma correction to the distances (by default \code{gamma =
- FALSE} so no correction is applied).}
+ \item{gamma}{a value for the gamma parameter possibly used to apply a
+ correction to the distances (by default no correction is applied).}
\item{pairwise.deletion}{a logical indicating whether to delete the
sites with missing data in a pairwise way. The default is to delete
- the sites with at least one missing data for all sequences.}
+ the sites with at least one missing data for all sequences (ignored
+ if \code{model = "indel"} or \code{"indelblock"}).}
\item{base.freq}{the base frequencies to be used in the computations
- (if applicable, i.e. if \code{method = "F84"}). By default, the
- base frequencies are computed from the whole sample of sequences.}
+ (if applicable). By default, the base frequencies are computed from
+ the whole set of sequences.}
\item{as.matrix}{a logical indicating whether to return the results as
a matrix. The default is to return an object of class
\link[stats]{dist}.}
\item{\code{paralin}: }{Lake (1994) developed the paralinear distance which
can be viewed as another variant of the Barry--Hartigan distance.}
+
+ \item{\code{indel}: }{this counts the number of sites where there is an
+ insertion/deletion gap in one sequence and not in the other.}
+
+ \item{\code{indelblock}: }{same than before but contiguous gaps are
+ counted as a single unit. Note that the distance between \code{-A-} and
+ \code{A--} is 3 because there are three different blocks of gaps, whereas
+ the ``indel'' distance will be 2.}
}}
\value{
an object of class \link[stats]{dist} (by default), or a numeric