mafft: Run Multiple Sequence Alignment (MAFFT) on a Set of Sequences

In mhahsler/rMSA: Interface for Popular Multiple Sequence Alignment Tools

Run Multiple Sequence Alignment (MAFFT) on a Set of Sequences

Description

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

Usage

mafft(x, param="--auto")
mafft_help()

Arguments

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()).

Details

For installation details see: https://github.com/mhahsler/rMSA/blob/master/INSTALL

Value

An object of class DNAMultipleAlignment (see BioStrings).

Author(s)

Michael Hahsler

References

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

Examples

## 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)

mhahsler/rMSA documentation built on May 24, 2024, 3:36 p.m.