---
name: "glam2format"
section: "1"
platform: "linux"
package: "glam2"
version: "1064-10"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/glam2format"
---

# glam2format(1)

converts GLAM2 motifs to FASTA or MSF format

## NAME

glam2format - converts GLAM2 motifs to FASTA or MSF format

## SYNOPSIS

**glam2format** \[**options**\] **my\_format** *my\_motif.glam2*

Formats: fasta, msf.

## DESCRIPTION

**glam2format** reads in a motif found by **glam2**, and writes it in a standard alignment format (FASTA-with-gaps or MSF). This enables the alignment to be passed to third-party software, including graphical visualization tools such as Kalignvu, Boxshade, and WebLogo. On the other hand, not all the motif information is preserved: in particular, the key positions are lost. Only the top motif in **glam2** output is converted.

## OPTIONS (DEFAULT SETTINGS)

**-o**

Output file (*stdout*).

**-c**

Make a compact alignment. By default, residues that are inserted between key positions are written as unaligned with each other. This best reflects **glam2**´s intention, but it can make the alignment large and full of gaps. With *-c*, inserted residues are written as arbitrarily aligned with each other, just as they appear in the **glam2** output.

**-f**

Sequence file to make a “global” alignment by adding flanking sequences from the original FASTA-format sequence file. The flanking sequences will be written as either unaligned with each other or arbitrarily aligned, depending on the *-c* option. The sequences should have unique names and their order should be unchanged.

## SEE ALSO

[**boxshade**(1)](/boxshade/1.md), [**glam2**(1)](/glam2/1.md), [**glam2mask**(1)](/glam2mask/1.md), [**glam2-purge**(1)](/glam2-purge/1.md), [**glam2scan**(1)](/glam2scan/1.md)

The full Hypertext documentation of GLAM2 is available online at *http://bioinformatics.org.au/glam2/* or on this computer in */usr/share/doc/glam2/*.

## REFERENCE

If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press).

## AUTHORS

**Martin Frith**

-

  Author of GLAM2.

**Timothy Bailey**

-

  Author of GLAM2.

**Charles Plessy** \<plessy@debian.org\>

-

  Formatted this manpage in DocBook XML for the Debian distribution.

## COPYRIGHT

The source code and the documentation of GLAM2 are released in the public domain.