xenial (1) afetch.1.gz

NAME

       afetch - retrieve an alignment from an alignment database

SYNOPSIS

       afetch [options] alignmentdb key

       afetch --index alignmentdb

DESCRIPTION

       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 (AC).

       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.

OPTIONS

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

EXPERT OPTIONS

       --index
              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.

SEE ALSO

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

AUTHOR

       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
       Email: eddy@genetics.wustl.edu