macroape software allows efficient comparison of transcription factor binding models (often called motifs) represented as position weight matrices (PWM) with given score thresholds.
[HOT] Check the corresponding paper in Algorithms Mol Biol.
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)
hocomoco v9 to be used with macroape
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.