Repository for using coverage heuristics for motif selection.
#Under the utils folder FIMO, Tomtom are part of the MEME suite: http://meme-suite.org/ FIMO is used for motif scanning. Charles E. Grant, Timothy L. Bailey, and William Stafford Noble, "FIMO: Scanning for occurrences of a given motif", Bioinformatics 27(7):1017–1018, 2011.
Tomtom is used for motif comaprison. Shobhit Gupta, JA Stamatoyannopolous, Timothy Bailey and William Stafford Noble, "Quantifying similarity between motifs", Genome Biology, 8(2):R24, 2007.
Template.eps and meme2images are part of MEME suite: http://meme-suite.org/