A software platform to perform in silico analyses of DNA methylation at cytosine sites. CyMATE is suitable for analyses of sequence data obtained with bisulfite genomic sequencing and hairpin-bisulfite sequencing, i.e. single-strand and double-strand DNA data. A module for mutation analysis at non-methylation sites is also available. It has been designed as a universal tool for quick, comprehensive and automated analysis of bisulfite sequencing data, providing detailed qualitative and quantitative results. Analysis with CyMATE is simple, very fast, platform-independent and the most detailed of computational analysis methods.