PyClone is a tool for inferring the cellular prevalence of point mutations from deeply sequenced data. It serves as a statistical model for inference of clonal population structures in cancers.The model supports simultaneous analysis of multiple related samples and infers clusters of mutations whose cellular prevalences shift together. Such clusters of mutations can be inferred as mutational genotypes of distinct clonal populations (Roth et al., Nature Meth 11, 396, 2014). Registration required.