msaClustalOmega {msa} | R Documentation

## 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

`inputSeqs` | input sequences; see `msa`. In the original ClustalOmega implementation, this parameter is called `infile`.
`cluster` | The cluster size which should be used. The default is 100. In the original ClustalOmega implementation, this parameter is called `cluster-size`.
`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 `msa`. However, setting these parameters to values other than `"default"` will result in a warning.
`maxiters` | maximum number of iterations; the default value is 0 (no limitation). In the original ClustalOmega implementation, this parameter is called `iterations`.
`substitutionMatrix` | name of substitution matrix for scoring matches and mismatches; can be one of the choices `"BLOSUM30"`, `"BLOSUM40"`, `"BLOSUM50"`, `"BLOSUM65"`, `"BLOSUM80"`, and `"Gonnet"`. This parameter is a new feature - the original ClustalOmega implementation does not allow for using a custom substitution matrix.
`type` | type of the input sequences `inputSeqs`; see `msa`.
`order` | how the sequences should be ordered in the output object (see `msa`); in the original ClustalW implementation, this parameter is called `output-order`.
`verbose` | if `TRUE`, the algorithm displays detailed information and progress messages.
`help` | if `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.
`...` | further parameters specific to ClustalOmega; An overview of parameters that are available in this interface is shown when calling `msaClustalOmega` with `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 `inputSeqs` argument above). Parameters that are common to all multiple sequences alignments provided by the 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 `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 `msa`.

### Value

Depending on the type of sequences for which it was called, `msaClustalOmega` returns a `MsaAAMultipleAlignment`, `MsaDNAMultipleAlignment`, or `MsaRNAMultipleAlignment` object. If called with `help=TRUE`, `msaClustalOmega` returns an invisible `NULL`.

### Author(s)

Enrico Bonatesta and Christoph Horejs-Kainrath <msa@bioinf.jku.at>

### References

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. Bioinformatics 31(24):3997-3999. DOI: 10.1093/bioinformatics/btv494.

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. Mol. Syst. Biol. 7:539. DOI: 10.1038/msb.2011.75.

### See Also

`msa`, `MsaAAMultipleAlignment`, `MsaDNAMultipleAlignment`, `MsaRNAMultipleAlignment`, `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)

[Package msa version 1.14.0 Index]