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

# glam2(1)

Gapped Local Alignment of Motifs

## NAME

glam2 - Gapped Local Alignment of Motifs

## SYNOPSIS

**glam2** \[**options**\] **alphabet** *my\_seqs.fa*

An alphabet other than *p* or *n* is interpreted as the name of an alphabet file.

## DESCRIPTION

GLAM2 is a software package for finding motifs in sequences, typically amino-acid or nucleotide sequences. A motif is a re-occurring sequence pattern: typical examples are the TATA box and the CAAX prenylation motif. The main innovation of GLAM2 is that it allows insertions and deletions in motifs.

## OPTIONS (DEFAULT SETTINGS)

**-h**

Show all options and their default settings.

**-o**

Output file (*stdout*).

**-r**

Number of alignment runs (*10*).

**-n**

End each run after this many iterations without improvement (*10000*).

**-2**

Examine both strands - forward and reverse complement.

**-z**

Minimum number of sequences in the alignment (*2*).

**-a**

Minimum number of aligned columns (*2*).

**-b**

Maximum number of aligned columns (*50*).

**-w**

Initial number of aligned columns (*20*).

**-d**

Dirichlet mixture file.

**-D**

Deletion pseudocount (*0.1*).

**-E**

No-deletion pseudocount (*2.0*).

**-I**

Insertion pseudocount (*0.02*).

**-J**

No-insertion pseudocount (*1.0*).

**-q**

Weight for generic versus sequence-set-specific residue abundances (*1e+99*).

**-t**

Initial temperature (*1.2*).

**-c**

Cooling factor per n iterations (*1.44*).

**-u**

Temperature lower bound (*0.1*).

**-p**

Print progress information at each iteration.

**-m**

Column-sampling moves per site-sampling move (*1.0*).

**-x**

Site sampling algorithm: *0*=FAST *1*=SLOW *2*=FFT (*0*).

**-s**

Seed for pseudo-random numbers (*1*).

## SEE ALSO

[**glam2format**(1)](/glam2format/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.