EDNA
Energy Based Multiple Sequence Alignment (MSA) for Binding Sites
Multiple Sequence Alignment for Transcription Factor Binding Sites using Di nucleotides dependencies and relying on Free Interaction energies between neighbouring DNA bases to stabilise substitution energy of the alignment.
http://www.ncbi.nlm.nih.gov/pubmed/23990411