MUSCLE: Run Multiple Sequence Alignment (MUSCLE) on a Set of...

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

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

Description

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

Usage

muscle(x, param="")
muscle_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 musce_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

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

Examples

## 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)

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