\name{msaClustalW}
\alias{msaClustalW}
\title{Multiple Sequence Alignment with ClustalW}
\description{
This function calls the multiple sequence alignment
algorithm ClustalW.
}
\usage{
msaClustalW(inputSeqs, cluster="default", gapOpening="default",
gapExtension="default", maxiters="default",
substitutionMatrix="default", type="default",
order=c("aligned", "input"), verbose=FALSE,
help=FALSE, ...)
}
\arguments{
In the original ClustalW implementation, this
parameter is called \code{infile}.}
\item{cluster}{The clustering method which should be used.
Possible values are \code{"nj"} (default) and \code{"upgma"}.
In the original ClustalW implementation, this parameter is called
\code{clustering}.}
\item{gapOpening}{gap opening penalty; the default value for
nucleotide sequences is 15.0, the default value for
amino acid sequences is 10.0.}
\item{gapExtension}{gap extension penalty; the default value for
nucleotide sequences is 6.66, the default value for
amino acid sequences is 0.2.}
\item{maxiters}{maximum number of iterations; the default value is 16.
In the original ClustalW implementation, this parameter is called
\code{numiters}.}
\item{substitutionMatrix}{substitution matrix for scoring matches and
mismatches; can be a real matrix, a file name, or the name of a
built-in substitution matrix. In the latter case, the choices
\code{"blosum"}, \code{"pam"}, \code{"gonnet"}, and \code{"id"} are
supported for amino acid sequences. For aligning nucleotide
sequences, the choices \code{"iub"} and \code{"clustalw"} are
possible. The parameter \code{dnamatrix} can also be used instead
for the sake of backwards compatibility.
The valid choices for this parameter are \code{"iub"} and
\code{"clustalw"}. In the original ClustalW implementation, this
parameter is called \code{matrix}.}
\item{type}{type of the input sequences \code{inputSeqs};
\item{order}{how the sequences should be ordered in the output object
(see \code{\link{msa}}); in the original ClustalW implementation, this
parameter is called \code{outorder}.}
\item{verbose}{if \code{TRUE}, the algorithm displays detailed
information and progress messages.}
parameters is displayed. In this case, no multiple sequence
alignment is performed and the function quits after displaying
\item{...}{further parameters specific to ClustalW;
An overview of parameters that are available in this interface
is shown when calling \code{msaClustalW} with \code{help=TRUE}.
}
\details{This is a function providing the ClustalW multiple alignment
algorithm as an R function. It can be used for various types of
sequence data (see \code{inputSeqs} argument above). Parameters that
are common to all multiple sequences alignments provided by the
\pkg{msa} package are explicitly provided by the function and named
in the same for all algorithms. Most other parameters that are
specific to ClustalW can be passed to ClustalW via additional
arguments (see argument \code{help} above).

For a note on the order of output sequences and direct reading from
}
\value{
Depending on the type of sequences for which it was called,
If called with \code{help=TRUE}, \code{msaClustalW} returns
an invisible \code{NULL}.
}
\author{Enrico Bonatesta and Christoph Horejs-Kainrath
<msa@bioinf.jku.at>
}
\references{
\url{http://www.bioinf.jku.at/software/msa}

U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter
(2015). msa: an R package for multiple sequence alignment.
\emph{Bioinformatics} \bold{31}(24):3997-3999. DOI:
\href{http://dx.doi.org/10.1093/bioinformatics/btv494}{10.1093/bioinformatics/btv494}.

Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994)
CLUSTAL W: improving the sensitivity of progressive multiple sequence
alignment through sequence weighting, position-specific gap penalties
and weight matrix choice.
\emph{Nucleic Acids Res.} \bold{22}(22):4673-4680. DOI:
\href{http://dx.doi.org/10.1093/nar/22.22.4673}{10.1093/nar/22.22.4673}.
}
}
\examples{