Summary: 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.
Family: GLAM2 is a child of GLAM and a sibling of A-GLAM. If you are looking for nucleotide motifs without insertions or deletions, A-GLAM is probably better. 'GLAM' used to stand for Gapless Local Alignment of Multiple sequences, but it now stands for Gapped Local Alignment of Motifs.
These are command line programs, so you need a basic familiarity with running things from your computer's command line in order to use them. (In Mac OS X, you want Applications -> Utilities -> Terminal.)
About: GLAM2 was developed by Martin C Frith, working at the Computational Biology Research Center in Tokyo, and Timothy L Bailey, working at the Institute for Molecular Bioscience in Brisbane. The source code and documentation are hereby released into the public domain. 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).
Contact: Questions and comments are welcome. Email: glam2(at-mark)imb.uq.edu.au. We would especially like to hear about any errors when installing or running the software (e.g. segmentation faults, assertion failures) so that we can fix them. Please send the exact text of the error message, and the exact inputs that produce the error.