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Converting alignment formats ACONVERT

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

Geoff Barton