***Introduction***           

The  MEME suite provides online 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. 

The MEME suite consists of programs which allow you to: 

* MEME      - for discovery of motifs shared by a group of sequences, 
* STREME    - for discovery expression motifs in large datasets
* MEME-ChIP - for analysis of large DNA datasets like ChIPseq output,
* GLAM2     - for discovery of gapped motifs,
* MoMo      - for finding post-translationally modified protein motifs,
* DREME     - [deprecated] for discovery of short regular expression motifs,
* CentriMo  - for central enrichment analysis of motifs,
* AME       - for general enrichment analysis of motifs,
* SpaMo     - for finding motif complexes by analysing motif spacing,
* GOMo      - for finding Gene Ontology terms linked to the motifs,
* FIMO      - for scanning sequences with motifs,
* MAST      - for scanning sequences to find groups of motifs,
* MCAST     - for scanning sequences for motif clusters,
* GLAM2scan - for scanning sequences with gapped motifs,
* Tomtom    - for comparing motifs to other motifs,
* T-Gene    - for predicting regulatory links between genomic loci and genes

and that's just the web enabled tools.

You can download the C source code for MEME suite from
https://meme-suite.org/meme/doc/download.html

You can also use the MEME suite via its website at https://meme-suite.org .

***Citing***

To cite the full MEME suite, please cite:  
> 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:  
    https://meme-suite.org/meme/doc/cite.html  


***Installation***       

See `doc/install.html` for operating system requirements, prerequisite
software, and installation instructions.

***Documentation***

Documentation is available online at https://meme-suite.org/meme/doc/overview.html
otherwise look in the `doc/` folder for `overview.html` as a place to start.  
If you did installation with the `--enable-web` switch, the html documentation
will be installed with the website at `<website>/meme_<version>/doc/overview.html`. 

***Problems and comments*** 

Please address any problems or comments to:  
    meme-suite@uw.edu 
or  
    https://groups.google.com/forum/#!forum/meme-suite  

***Release Notes***

See file `<distribution-path>/doc/release-notes.html`  
or after a basic install see `<install-path>/doc/release_notes.html`  
or for a website install see `<website>/meme_<version>/doc/release-notes.html`  
