Ok. Thank you very much. I will try with muscle. Álvaro Pena 2010/1/19 Peter Cock <p.j.a.cock at googlemail.com> > Hi, > > I'm a little unclear what you are trying to do - clustalw doesn't let > you send input via stdin or get the alignment by stdout. Other tools > like muscle can do this and our tutorial has examples of this. > > Peter >