GLAM2(1)							   glam2 Manual 							  GLAM2(1)

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), glam2mask(1), glam2-purge(1), glam2scan(1)

       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.

GLAM2 1056							    05/19/2008								  GLAM2(1)