I'm happy to announce the latest release of GimmeMotifs (0.11.1)
GimmeMotifs is an analysis framework for transcription factor motif analysis written in Python. It contains command-line scripts to predict de novo motifs, scan for known motifs, identify differential motifs, calculate motif enrichment statistics, plot sequence logos and more. In addition, all this functionality is available from a Python API.
While it was originally developed as an ensemble approach to discover de novo motif from ChIP-seq data (and still does very well at that), it can do much more.
The github repository is here: https://github.com/simonvh/gimmemotifs
The documentation is here: http://gimmemotifs.readthedocs.io/
Try it out, and let me know your thoughts, bugs and issues.