align.muscle:
Multiple sequence alignment by means of Muscle (MUltiple Sequence Comparison by Log-Expectation)
Description
DNA sequences are aligned by means of Muscle Version 3.8. (Multiple Sequences Alignment)
Usage
align.muscle(filein , fileout = "Sq.fa", gapopen = gapopen, maxiters = maxiters, gapextend = gapextend, call)
Arguments
filein
A set of nucleotide sequences in FASTA format.
fileout
Output file in FASTA format.
maxiters
Maximum number of iterations.
gapextend
Gap extend score.
call
string of characters needed to call Muscle from the working directory
Details
Gapopen and gapextend must be negative. Output is a file in FASTA format with aligned nucleotide sequences. This function needs aaMI-package.
See Also
align.clustalw, align.MEME