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Motivation: Recent studies sequenced tumor samples from the same progenitor at different devel-opment stages and showed that by taking into account the phylogeny of this development, single-nucleotide variant (SNV) calling can be improved. Accurate SNV calls can better reveal early-stage tumors, identify mechanisms of cancer progression or help in drug targeting. Results: We present SNV-PPILP, a fast and easy to use tool for refining GATK’s Unified Genotyper SNV calls, for multiple samples assumed to form a phylogeny. We tested SNV-PPILP on simulated data, with a varying number of samples, SNVs, read coverage and violations of the perfect phylogeny assumption. We always match or improve the accuracy of GATK, with a significant improvement on low read coverage. Availability and implementation: SNV-PPILP, available at cs.helsinki.fi/gsa/snv-ppilp/, is written in Python and requires the free ILP solver lp_solve. Contact