A computer-implemented method includes inputting, to a processor, an N×K SSV frequency matrix M and an error tolerance δ≥0, wherein N is a number of SSVs and K is a number of time points, wherein matrix M comprises a plurality of time-resolved mutation frequencies for each SSV; clustering, by the processor, matrix rows in M that satisfy the δ to provide a plurality of SSV clusters; assigning, by the processor, a mean cluster frequency to each SSV within each SSV cluster; calculating errors for removing low frequency rows, for rounding rows to 1 or 0; assigning a root node for all SSV clusters of frequency 1; and calculating, by the processor, a δ-compliant time-series evolution tree with error ≤δ comprising the root node and a plurality time-stratified nodes, wherein calculating includes assigning a clonal configuration, optionally re-configuring the clonal configuration, and calculating error for re-configuring.