The MEME suite: motif based sequence analysis tools

The MEME suite provides tools for discovering and using protein and
DNA sequence motifs.  A motif is a pattern of nucleotides or amino acids
that appears repeatedly in a group of related DNA or protein sequences.

The MEME suite represents motifs as position-dependent scoring matrices.
It consists of programs which allow you to:

- meme      - discovery of motifs shared by a group of sequences
- mast      - search of databases for sequences containing these motifs
- tomtom    - searching databases of motifs for similar motifs
- gomo      - finding Gene Ontology terms linked to the motifs
- glam2     - discovery of gapped motifs
- glam2scan - scanning sequences with gapped motifs
- fimo      - scanning sequences with motifs
- mcast     - finding motif clusters
- meme-chip - analysis of large DNA datasets like ChIPseq output
- spamo     - finding motif complexes by analysing motif spacing
- dreme     - discovery of short regular expression motifs

Note: building on a 32bit architecture fails at the 'make test' step
(check script). If the step is disabled, the suite builds, however it
may or may NOT work properly. Therefore, 32bit is set as 'UNTESTED'.
The 'make test' step will also fail if you don't build in a proper root
environment.

To cite the full MEME suite:
Timothy L. Bailey, Mikael Bodén, Fabian A. Buske, Martin Frith,
Charles E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li,
William S. Noble, "MEME SUITE: tools for motif discovery and searching",
Nucleic Acids Research, 37:W202-W208, 2009.

To cite individual tools, please check the citation page:
http://meme-suite.org/doc/cite.html