kalign: Multiple Sequence Alignment (Kalign)
In mhahsler/rMSA: Interface for Popular Multiple Sequence Alignment Tools

kalign

R Documentation

Multiple Sequence Alignment (Kalign)

Description

Runs Kalign progressive multiple sequence alignment on a set of sequences.

Usage

kalign(x, param=NULL)
kalign_help()

Arguments

`x`	an object of class DNAStringSet with the sequences to be aligned.
`param`	character string with the command line parameters for kalign (see output of `kalign_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

Lassmann T., Sonnhammer E. Kalign - an accurate and fast multiple sequence alignment algorithm, BMC Bioinformatics 2005, 6:298

Examples

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

### align the sequences
al <- kalign(dna)
al

## End(Not run)

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