afetch1

Usage

Overview

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.

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.