Workflow of the BISMA software and summary of its result files. A) Uploading the reference sequence and the bisulfite sequencing data. B) Analysis of the sequencing data by BISMA using the user defined thresholds. Sequences which do not pass the user defined thresholds will be removed. C) Visualization of the alignment of all included sequences. Sequences which pass the filtering for clonal sequences will be pre-selected to be included for later analysis. D) Analysis of the methylation pattern in the user selected dataset. E) All result files can be downloaded in one ZIP file containing: 1) The sequence alignment in which the methylation pattern is highlighted. 2) A graphical representation of the methylation pattern in context of the CpG distribution in the reference sequence. Each DNA sequence is represented by a line and each CpG site by a box. 3) A condensed graphical representation of the methylation pattern. Each row corresponds to one DNA sequence while each column represents a CpG site. 4) A graphical representation of the average methylation at each CpG site. 5) The methylation statistics including the methylation level observed over all sequences and the number of CpG sites that were found to be informative. 6) The methylation levels of the individual sequences.