macroape software allows efficient comparison of transcription factor binding models (often called motifs) represented as position weight matrices (PWM) with given score thresholds.
To use macroape you need ruby >=1.9.3 installed. Most modern Linux distributions have ruby 1.9 available in package repositories. Windows users can directly go to the downloads section here.
manual v4.0 (pdf, docx)
Funding: This work was supported, in part, by a Dynasty Foundation Fellowship; Russian Foundation for Basic Research [12-04-32082-mol_a and 12-04-01736-a]; Program "Cell and Molecular Biology" of the Presidium of RAS.