muscle (version 3.14.0)

muscle: Multiple Sequence Alignment

Description

MUSCLE performs multiple sequence alignments of nucleotide or amino acid sequences.

Usage

muscle(stringset, quiet = FALSE, ...)

Arguments

stringset

An object of class XStringSet: DNAStringSet, RNAStringSet, or AAStringSet.

quiet

Logical, whether to prevent printing of the progress of the algorithm to the screen. Defaults to FALSE.

...

Arguments (options and flags) for the MUSCLE algorithm (see Details).

Value

Output is an object of class MultipleAlignment: DNAMultipleAlignment, RNAMultipleAlignment, or AAMultipleAlignment.

Details

Arguments for the MUSCLE algorithm are either options or flags. Options take a variety of values, but flags are always logicals (TRUE or FALSE). All options and flags are explained in detail on the MUSCLE website: http://www.drive5.com/muscle/muscle_userguide3.8.html

References

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

See Also

umax

Examples

## Align sequences in an XStringSet object.
aln <- muscle(stringset = umax)

## Switch on the diags flag.
aln <- muscle(stringset = umax, diags = TRUE)