Comparison of PhISCS with SCITE based on normalized MLTSM. (A) Normalized MLTSM values when no ISA violations are allowed and no bulk data used in PhISCS. (B) Normalized MLTSM values when ISA violations are allowed in PhISCS but bulk data is not part of the input. (C) Normalized MLTSM values when PhISCS employs both ISA violations and VAFs derived from the bulk data. In each case, 100 single cells were sampled and the total number of simulated mutations was set to 40. In C, one bulk sample was used and coverage of bulk data was set to 10,000×. SC and ISA, respectively, denote the number of subclones and the number of simulated mutations for which ISA is violated. These plots illustrate that PhISCS has comparable performance to SCITE in cases where only SCS data is used; however, the additional use of bulk data substantially improves the performance of PhISCS over SCITE.