Dear John, You could try the seqaln() function in the bio3d library: http://mccammon.ucsd.edu/~bgrant/bio3d/html/seqaln.html This makes a multiple alignment using the Muscle software. I think you need to have Muscle installed on your computer. Regards, Avril > On Fri, Nov 20, 2009 at 12:52 AM, John Lande <john.lande77 at="" gmail.com="" <https:="" stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > wrote: > > > dear all, > > > > is there a an implementation of clustalw in bioconductor? > > > > > > [[alternative HTML version deleted]]