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       afetch - retrieve an alignment from an alignment database


       afetch [options] alignmentdb key

       afetch --index alignmentdb


       afetch  retrieves the alignment named key from an alignment database in
       file alignmentdb.

       alignmentdb is a "multiple multiple alignment" file in Stockholm  (e.g.
       native Pfam) format.

       key  is  either the name (ID) of the alignment, or its accession number

       The alignmentdb file should first be SSI indexed  with  afetch  --index
       for  efficient  retrieval.  An SSI index is not required, but alignment
       retrieval without one may be painfully slow.


       -h     Print brief help; includes version number  and  summary  of  all
              options, including expert options.


              Instead  of retrieving a key, the special command afetch --index
              alignmentdb produces an SSI index of the names and accessions of
              the alignments in the file alignmentdb.  This should be run once
              on the alignmentdb file to prepare it for all future afetch’s.


       alistat(1),  compalign(1),  compstruct(1),   revcomp(1),   seqsplit(1),
       seqstat(1),    sfetch(1),    shuffle(1),    sindex(1),    sreformat(1),
       stranslate(1), weight(1).


       Biosquid  and   its   documentation   are   Copyright   (C)   1992-2003
       HHMI/Washington  University School of Medicine Freely distributed under
       the GNU General Public License (GPL) See COPYING  in  the  source  code
       distribution for more details, or contact me.

       Sean Eddy
       HHMI/Department of Genetics
       Washington University School of Medicine
       4444 Forest Park Blvd., Box 8510
       St Louis, MO 63108 USA
       Phone: 1-314-362-7666
       FAX  : 1-314-362-2157