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\name{clustal}
\alias{clustal}
\alias{clustalomega}
\alias{muscle}
\alias{muscle5}
\alias{tcoffee}
\alias{efastats}
\alias{letterconf}
\title{Multiple Sequence Alignment with External Applications}
\description{
These functions call their respective program from \R to align a set
of nucleotide sequences of class \code{"DNAbin"} or
\code{"AAbin"}. The application(s) must be installed seperately and it
is highly recommended to do this so that the executables are in a
directory located on the PATH of the system.
This version includes an experimental version of \code{muscle5} which
calls MUSCLE5 (see the link to the documentation in the References
below); \code{muscle} still calls MUSCLE version 3. Note that the
executable of MUSCLE5 is also named `muscle' by the default
compilation setting.
The functions \code{efastats} and \code{letterconf} require MUSCLE5.
}
\usage{
clustal(x, y, guide.tree, pw.gapopen = 10, pw.gapext = 0.1,
gapopen = 10, gapext = 0.2, exec = NULL, MoreArgs = "",
quiet = TRUE, original.ordering = TRUE, file)
clustalomega(x, y, guide.tree, exec = NULL,MoreArgs = "",
quiet = TRUE, original.ordering = TRUE, file)
muscle(x, y, guide.tree, exec, MoreArgs = "",
quiet = TRUE, original.ordering = TRUE, file)
muscle5(x, exec = "muscle", MoreArgs = "", quiet = FALSE,
file, super5 = FALSE, mc.cores = 1)
tcoffee(x, exec = "t_coffee", MoreArgs = "", quiet = TRUE,
original.ordering = TRUE)
efastats(X, exec = "muscle", quiet = FALSE)
letterconf(X, exec = "muscle")
}
\arguments{
\item{x}{an object of class \code{"DNAbin"} or \code{"AAbin"} (can be
missing).}
\item{y}{an object of class \code{"DNAbin"} or \code{"AAbin"} used for
profile alignment (can be missing).}
\item{guide.tree}{guide tree, an object of class \code{"phylo"} (can
be missing).}
\item{pw.gapopen, pw.gapext}{gap opening and gap extension penalties
used by Clustal during pairwise alignments.}
\item{gapopen, gapext}{idem for global alignment.}
\item{exec}{a character string giving the name of the program, with
its path if necessary. \code{clustal} tries to guess this argument
depending on the operating system (see details).}
\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} (\code{TRUE} by
default).}
\item{file}{a file with its path if results should be stored (can be
missing).}
\item{super5}{a logical value. By default, the PPP algorithm is used.}
\item{mc.cores}{the number of cores to be used by MUSCLE5.}
\item{X}{a list with several alignments of the same sequences with
all with the same row order.}
}
\details{
It is highly recommended to install the executables properly so that
they are in a directory located on the PATH (i.e., accessible from any
other directory). Alternatively, the full path to the executable
may be given (e.g., \code{exec = "~/muscle/muscle"}), or a (symbolic)
link may be copied in the working directory. For Debian and its
derivatives (e.g., Ubuntu), it is recommended to use the binaries
distributed by Debian.
\code{clustal} tries to guess the name of the executable program
depending on the operating system. Specifically, the followings are
used: ``clustalw'' under Linux, ``clustalw2'' under MacOS, and
``clustalw2.exe'' under Windows. For \code{clustalomega},
``clustalo[.exe]'' is the default on all systems (with no specific
path).
When called without arguments (i.e., \code{clustal()}, \dots), the
function prints the options of the program which may be passed to
\code{MoreArgs}.
Since \pkg{ape} 5.1, \code{clustal}, \code{clustalomega}, and
\code{muscle} can align AA sequences as well as DNA sequences.
}
\value{
an object of class \code{"DNAbin"} or \code{"AAbin"} with the aligned
sequences.
\code{efastats} returns a data frame.
\code{letterconf} opens the default Web brower.
}
\references{
Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T. J.,
Higgins, D. G. and Thompson, J. D. (2003) Multiple sequence alignment
with the Clustal series of programs. \emph{Nucleic Acids Research}
\bold{31}, 3497--3500. \url{http://www.clustal.org/}
Edgar, R. C. (2004) MUSCLE: Multiple sequence alignment with high
accuracy and high throughput. \emph{Nucleic Acids Research},
\bold{32}, 1792--1797.
\url{http://www.drive5.com/muscle/muscle_userguide3.8.html}
Notredame, C., Higgins, D. and Heringa, J. (2000) T-Coffee: A novel
method for multiple sequence alignments. \emph{Journal of Molecular
Biology}, \bold{302}, 205--217.
\url{https://tcoffee.org/}
Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W.,
Lopez, R., McWilliam, H., Remmert, M., S\"oding, J., Thompson,
J. D. and Higgins, D. G. (2011) Fast, scalable generation of
high-quality protein multiple sequence alignments using Clustal
Omega. \emph{Molecular Systems Biology}, \bold{7}, 539.
\url{http://www.clustal.org/}
\url{https://drive5.com/muscle5/}
}
\author{Emmanuel Paradis, Franz Krah}
\seealso{
\code{\link{image.DNAbin}}, \code{\link{del.gaps}},
\code{\link{all.equal.DNAbin}}, \code{\link{alex}},
\code{\link{alview}}, \code{\link{checkAlignment}}
}
\examples{
\dontrun{
### display the options:
clustal()
clustalomega()
muscle()
tcoffee()
data(woodmouse)
### open gaps more easily:
clustal(woodmouse, pw.gapopen = 1, pw.gapext = 1)
### T-Coffee requires negative values (quite slow; muscle() is much faster):
tcoffee(woodmouse, MoreArgs = "-gapopen=-10 -gapext=-2")
}}
\keyword{manip}
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