AutoClone is a shiny app for the automatic assessment of clonality based on the data generated through genetic cell labelling and lineage tracing assays. The AutoClone app includes three major modes relevant to the input data. The clonality assessment is a technique used to evaluate the similarity of cells/fibers generated through a biological process or through development. This technique can also be used for lineage tracing of cells/fibers during development. There are several methods for performing these analyses most of which rely on genetic cell labelling and coloring of the cells. One of the important aspects of labelling-based lineage tracing and clonal analysis is the quantification and statistical evaluation of the results (i.e. converting visual colors to interpretable statistics). The AutoClone app makes it possible for you to automatically perform these quantifications and statistical analyses.