MAtrix CompaRisOn and PrEdicting Regulatory Functional Effect by Approximate P-value Estimation toolbox allows estimating motif P-values, comparing PWMs using natural Jaccard similarity measure and motif-based analysis of regulatory SNVs for mono- and dinucleotide PWMs, read more here and there.
ChIPMunk is a fast heuristic DNA motif digger based a on greedy approach accompanied by bootstrapping. Now classic and dinucleotide versions come in a single updated package, read more.
Straightforward yet Powerful Rapid SuperAlphabet Representation Utilized for motif Search is as practical ChIPMunk companion, read more.
EpiFactors is a database for epigenetic factors, corresponding genes and products,
GenometriCorr is an R package for spatial correlation of genome-wide interval datasets,