align.muscle: Multiple sequence alignment by means of Muscle (MUltiple...
In MEET: MEET: Motif Elements Estimation Toolkit

Description Usage Arguments Details Author(s) References See Also Examples

DNA sequences are aligned by means of Muscle Version 3.8. (Multiple Sequences Alignment)

1	align.muscle(filein, fileout = "Sq.fa", gapopen , maxiters, gapextend , call)

`filein`	A set of nucleotide sequences in FASTA format.
`fileout`	Output file in FASTA format.
`gapopen`	Gap open score.
`maxiters`	Maximum number of iterations.
`gapextend`	Gap extend score.
`call`	string of characters needed to call Muscle from the working directory

Gapopen and gapextend must be negative. Output is a file in FASTA format with aligned nucleotide sequences. This function needs aaMI-package.

Erola Pairo <epairo@ibecbarcelona.eu> and Joan Maynou <joan.maynou@upc.edu>

R. C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res, vol. 32, no. 5, 2004. [Online]. Available: http://dx.doi.org/10.1093/nar/ gkh340

align.clustalw, align.MEME

1 2	pathMEET<-system.file("exdata",package="MEET") #align.muscle(filein=paste(pathMEET,"AP1.fa",sep="/"), fileout="Sq.fa", gapen=-12, maxiters=16, gapextend=-1, call="muscle")