Bisulfighter is a software package for detecting methylated cytosines (mCs) and differentially methylated regions (DMRs) from bisulfite sequencing data.
URL: http://epigenome.cbrc.jp/bisulfighter
Saito Y, Tsuji J, Mituyama T. Bisulfighter: accurate detection of methylated cytosines and differentially methylated regions. Nucleic Acids Res. 42, e45 (2014).