R Graphical Manual

Last data update: 2014.03.03

R: Multiple sequence alignment by means of Muscle (MUltiple...

align.muscle

R Documentation

Multiple sequence alignment by means of Muscle (MUltiple Sequence Comparison by Log-Expectation)

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

align.muscle(filein , fileout = "Sq.fa", gapopen = gapopen, maxiters = maxiters, gapextend = 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 <epeiroatibec.pcb.ub.es> and Joan Maynou <joan.maynouatupc.edu>