A collection of tools to deal with Bisulfite-seq/NOMe-seq

BisSNP: Accurate combined SNP/Methylation calling.

DMNTools: HMM segmentation (NDR/Nucleosome positioning detection, HMR detection for DNA methylation)

alignWigToBed: Visualization/Clustering (Align signal in wiggler file to a group of genomic location and visulize them)