mafft: Run Multiple Sequence Alignment (MAFFT) on a Set of Sequences
In mhahsler/rMSA: Interface for Popular Multiple Sequence Alignment Tools

Description Usage Arguments Details Value Author(s) References Examples

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

1 2	mafft(x, param="--auto") mafft_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 `mafft_help()`).

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

An object of class DNAMultipleAlignment (see BioStrings).

Michael Hahsler

Katoh, Standley 2013 (Molecular Biology and Evolution 30:772-780) MAFFT multiple sequence alignment software version 7: improvements in performance and usability.

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

al <- mafft(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 <- mafft(rna)
al

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

al <- mafft(aa)
al

## End(Not run)