The MethPipe software package is a computational pipeline for analyzing bisulfite sequencing data (BS-seq, WGBS and RRBS). MethPipe provides tools for mapping bisulfite sequencing read and estimating methylation levels at individual cytosine sites. Additionally, MethPipe includes tools for identifying higher-level methylation features, such as hypo-methylated regions (HMR), partially methylated domains (PMD), hyper-methylated regions (HyperMR), and allele-specific methylated regions (AMR).