msaMuscle {msa} | R Documentation

## Multiple Sequence Alignment with MUSCLE

### Description

This function calls the multiple sequence alignment algorithm MUSCLE.

### Usage

        msaMuscle(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 MUSCLE implementation, this parameter is called `-in`.
`cluster` | The clustering method which should be used. Possible values are `"upgma"`, `"upgmamax"`, `"upgmamin"`, `"upgmb"`, and `"neighborjoining"`.
`gapOpening` | gap opening penalty; the default is 400 for DNA sequences and 420 for RNA sequences. The default for amino acid sequences depends on the profile score settings: for the setting `le=TRUE`, the default is 2.9, for `sp=TRUE`, the default is 1,439, and for `sv=TRUE`, the default is 300. Note that these defaults may not be suitable if custom substitution matrices are being used. In such a case, a sensible choice of gap penalties that fits well to the substitution matrix must be made.
`gapExtension` | gap extension penalty; the default is 0.
`maxiters` | maximum number of iterations; the default is 16. In the original MUSCLE implementation, it is also possible to set `maxiters` to 0 which leads to an (out of memory) error. Therefore, `maxiters=0` is not allowed in `msaMuscle`.
`substitutionMatrix` | substitution matrix for scoring matches and mismatches; can be a real matrix or a file name If the file interface is used, matrices have to be in NCBI-format. The original MUSCLE implementation also accepts matrices in WU_BLAST (AB_BLAST) format, but, due to copyright restrictions, this format is not supported by `msaMuscle`.
`type` | type of the input sequences `inputSeqs`; see `msa`.
`order` | how the sequences should be ordered in the output object (see `msa` for more details); the original MUSCLE implementation does not allow for preserving the order of input sequences. The `msaMuscle` function realizes this functionality by reverse matching of sequence names. Therefore, the sequences need to have unique names. If the sequences do not have names or if the names are not unique, the `msaMuscle` function assignes generic unique names `"Seq1"`-`Seqn` to the sequences and issues a warning. The choice `"input"` is not available at all for sequence data that is read directly from a FASTA file.
`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 MUSCLE; An overview of parameters that are available in this interface is shown when calling `msaMuscle` with `help=TRUE`. For more details, see also the documentation of MUSCLE.

### Details

This is a function providing the MUSCLE 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 MUSCLE can be passed to MUSCLE via additional arguments (see argument `help` above).

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, `msaMuscle` returns a `MsaAAMultipleAlignment`, `MsaDNAMultipleAlignment`, or `MsaRNAMultipleAlignment` object. If called with `help=TRUE`, `msaMuscle` 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.drive5.com/muscle/muscle.html

Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(5):1792-1797. DOI: 10.1093/nar/gkh340.

Edgar, R. C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113. DOI: 10.1186/1471-2105-5-113.

### See Also

`msa`, `MsaAAMultipleAlignment`, `MsaDNAMultipleAlignment`, `MsaRNAMultipleAlignment`, `MsaMetaData`

### Examples

    ## read sequences
    filepath <- system.file("examples", "exampleAA.fasta", package="msa")
    mySeqs <- readAAStringSet(filepath)

    ## call msaMuscle with default values
    msaMuscle(mySeqs)

    ## call msaMuscle with custom parameters
    msaMuscle(mySeqs, gapOpening=12, gapExtension=3, maxiters=16,
              cluster="upgmamax", SUEFF=0.4, brenner=FALSE,
              order="input", verbose=FALSE)

    ## call msaMuscle with a custom substitution matrix
    data(PAM120)
    msaMuscle(mySeqs, substitutionMatrix=PAM120)

[Package msa version 1.18.0 Index]