---
name: "afetch"
section: "1"
platform: "linux"
package: "biosquid"
version: "1.9g+cvs20050121-15.1+b2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/afetch"
---

# afetch(1)

## 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)](/alistat/1.md), [**compalign**(1)](/compalign/1.md), [**compstruct**(1)](/compstruct/1.md), [**revcomp**(1)](/revcomp/1.md), [**seqsplit**(1)](/seqsplit/1.md), [**seqstat**(1)](/seqstat/1.md), [**sfetch**(1)](/sfetch/1.md), [**shuffle**(1)](/shuffle/1.md), [**sindex**(1)](/sindex/1.md), [**sreformat**(1)](/sreformat/1.md), [**stranslate**(1)](/stranslate/1.md), [**weight**(1)](/weight/1.md).

## 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
```