\usage{
clustal(x, pw.gapopen = 10, pw.gapext = 0.1,
gapopen = 10, gapext = 0.2, exec = NULL,
- MoreArgs = "", quiet = TRUE)
-muscle(x, exec = "muscle", MoreArgs = "", quiet = TRUE)
-tcoffee(x, exec = "t_coffee", MoreArgs = "", quiet = TRUE)
+ MoreArgs = "", quiet = TRUE, original.ordering = TRUE)
+muscle(x, exec = "muscle", MoreArgs = "", quiet = TRUE,
+ original.ordering = TRUE)
+tcoffee(x, exec = "t_coffee", MoreArgs = "", quiet = TRUE,
+ original.ordering = TRUE)
}
\arguments{
\item{x}{an object of class \code{"DNAbin"}.}
\item{MoreArgs}{a character string giving additional options.}
\item{quiet}{a logical: the default is to not print on \R's console the
messages from the external program.}
+ \item{original.ordering}{a logical specifying whether to return the
+ aligned sequences in the same order than in \code{x}.}
}
\details{
\code{clustal} tries to guess the name of the executable program
}
\author{Emmanuel Paradis}
\seealso{
- \code{\link{image.DNAbin}}, \code{\link{del.gaps}}
+ \code{\link{image.DNAbin}}, \code{\link{del.gaps}}, \code{\link{alex}}
The package \pkg{phyloch} which has similar functions for the MAFFT
and Prank.