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)