What it does
Compare two collections of position-specific scoring matrices (PSSM), and return various similarity statistics + matrix alignments (pairwise, one-to-n).
For the underlying tool, please cite Thomas-Chollier, M., Defrance, M., Medina-Rivera, A., Sand, O., Herrmann, C., Thieffry, D. and van Helden, J. (2011). RSAT 2011: regulatory sequence analysis tools. Nucleic Acids Research doi: 10.1093/nar/gkr377.