MUSCLE: Run Multiple Sequence Alignment (MUSCLE) on a Set of...
In mhahsler/rMSA: Interface for Popular Multiple Sequence Alignment Tools

Description Usage Arguments Details Value Author(s) References Examples

Executes MUSLCE on a set of sequences to obtain a multiple sequence alignment.

1 2	muscle(x, param="") muscle_help()

`x`	an object of class XStringSet (e.g., DNAStringSet) with the sequences to be aligned.
`param`	character string with the command line parameters (see output of `musce_help()`).

The MUSCLE software has to be installed (see rMSA_INSTALL).

An object of class DNAMultipleAlignment (see BioStrings).

Michael Hahsler

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

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

## Not run: 
### DNA
dna <- readDNAStringSet(system.file("examples/DNA_example.fasta",
	package="rMSA"))
dna

al <- muscle(dna)
al

### inspect alignment
detail(al)

### plot a sequence logo for the first 20 positions
plot(al, 1, 20)

### RNA
rna <- readRNAStringSet(system.file("examples/RNA_example.fasta",
	package="rMSA"))
rna

al <- MUSCLE(rna)
al

### Proteins
aa <- readAAStringSet(system.file("examples/Protein_example.fasta",
	package="rMSA"))
aa

al <- MUSCLE(aa)
al

## End(Not run)