MONKEY is a set of programs designed to search alignments of non-coding DNA sequence for matches to matrices representing the sequence specificity of transcription factors

Check out the original MONKEY paper: Moses et. al. Genome Biol. 2004;5(12):R98 view supplementary figures

rMONKEY is now published: Moses et al. PLoS comput Biol. 2006 Oct 13;2(10)

note that there are some problems with this manuscript:
1) Formatting of table 1 is wrong so find these number in the text
2) the links to the supplementary data files on the PLoS website are reversed

download the latest release
download the documentation
release notes:

8/8/06 - release 2.0, now includes rmonkey 

4/4/06 - doc file updated