A perl utility is now included in the STAMP package. In the STAMPDIR/bin directory you should find a perl program called ACONVERT. This program converts various alignment formats back and forth. The format is:
aconvert [-in <type> -out <type>] < <input file> > <output file>
where `type' is one of `c', `m', `b', `f', `p', which denote CLUSTAL, MSF, BLOCK,
FASTA and PIR format respectively. If no `-in' argument is given, the program tries
to guess the format, though note that this can sometimes fail (the program will usually
tell you). So to convert a STAMP alignment into CLUSTAL format, you type (e.g.):
aconvert -in b -out c < stamp_trans.10 > stamp_trans.10.aln