\name{msaClustalOmega}
 \alias{msaClustalOmega}
 \title{Multiple Sequence Alignment with ClustalOmega}
 \description{
   This function calls the multiple sequence alignment
   algorithm ClustalOmega.
 }
 \usage{
     msaClustalOmega(inputSeqs, cluster="default",
                     gapOpening="default", gapExtension="default",
                     maxiters="default",  substitutionMatrix="default",

                     type="default", order=c("aligned", "input"),
                     verbose=FALSE, help=FALSE, ...) 

 }
 \arguments{
   \item{inputSeqs}{input sequences; see \code{\link{msa}}.
     In the original ClustalOmega implementation, this

     parameter is called \code{infile}.}

   \item{cluster}{The cluster size which should be used. The default is 100.  
     In the original ClustalOmega implementation, this parameter is called 

     \code{cluster-size}.}
   \item{gapOpening,gapExtension}{ClustalOmega currently does
     not allow to adjust gap penalties; these arguments are only for
     future extensions and consistency with the other algorithms
     and \code{\link{msa}}. However, setting these parameters to values
     other than \code{"default"} will result in a warning.}

   \item{maxiters}{maximum number of iterations; the default value is 0
     (no limitation). In the original ClustalOmega implementation, this

     parameter is called \code{iterations}.}

   \item{substitutionMatrix}{name of substitution matrix for scoring matches and
     mismatches; can be one of the choices

     \code{"BLOSUM30"}, \code{"BLOSUM40"}, \code{"BLOSUM50"},

     \code{"BLOSUM65"}, \code{"BLOSUM80"}, and \code{"Gonnet"}.
     This parameter is a new feature - the original ClustalOmega

     implementation does not allow for using a custom substitution matrix.}
   \item{type}{type of the input sequences \code{inputSeqs};
     see \code{\link{msa}}.}

   \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{output-order}.}

   \item{verbose}{if \code{TRUE}, the algorithm displays detailed
     information and progress messages.}
   \item{help}{if \code{TRUE}, information about algorithm-specific
     parameters is displayed. In this case, no multiple sequence
     alignment is performed and the function quits after displaying
     the additional help information.}
   \item{...}{further parameters specific to ClustalOmega;
     An overview of parameters that are available in this interface
     is shown when calling \code{msaClustalOmega} with \code{help=TRUE}.
     For more details, see also the documentation of ClustalOmega.}
 }
 \details{This is a function providing the ClustalOmega 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 ClustalOmega can be passed to ClustalOmega via additional
   arguments (see argument \code{help} above).
 

   Since ClustalOmega only allows for using built-in amino acid
   substitution matrices, it is hardly useful for multiple alignments
   of nucleotide sequences.
 

   For a note on the order of output sequences and direct reading from
   FASTA files, see \code{\link{msa}}.
 }
 \value{
    Depending on the type of sequences for which it was called,
    \code{msaClustalOmega} returns a
    \code{\linkS4class{MsaAAMultipleAlignment}}, 
    \code{\linkS4class{MsaDNAMultipleAlignment}}, or
    \code{\linkS4class{MsaRNAMultipleAlignment}} object.
    If called with \code{help=TRUE}, \code{msaClustalOmega} 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}.

 
   \url{http://www.clustal.org/omega/README}
   
   Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W.,
   Lopez, R., McWilliam, H., Remmert, M., Soeding, J., Thompson, J. D.,
   and Higgins, D. G. (2011) Fast, scalable generation of high-quality
   protein multiple sequence alignments using Clustal Omega.
   \emph{Mol. Syst. Biol.} \bold{7}:539. DOI:
   \href{http://dx.doi.org/10.1038/msb.2011.75}{10.1038/msb.2011.75}.
 }
 \seealso{\code{\link{msa}}, \code{\linkS4class{MsaAAMultipleAlignment}},
   \code{\linkS4class{MsaDNAMultipleAlignment}},
   \code{\linkS4class{MsaRNAMultipleAlignment}},
   \code{\linkS4class{MsaMetaData}}
 }
 \examples{
 ## read sequences
 filepath <- system.file("examples", "exampleAA.fasta", package="msa")
 mySeqs <- readAAStringSet(filepath)
 
 ## call msaClustalOmega with default values
 msaClustalOmega(mySeqs)
 
 ## call msaClustalOmega with custom parameters

 msaClustalOmega(mySeqs, auto=FALSE, cluster=120, dealign=FALSE,
                 useKimura=FALSE, order="input", verbose=FALSE)

 }
 \keyword{manip}