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

Description Usage Arguments Details Value Author(s) References Examples

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

1 2	kalign(x, param=NULL) kalign_help()

`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()`).

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

An object of class DNAMultipleAlignment (see BioStrings).

Michael Hahsler

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

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

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

## End(Not run)