 The paper presents a new phylogenetic model called CICA specifically designed for scalable single-cell whole genome sequencing, SCWGS, data, which allows for unprecedented high-resolution measurement of cancer cell population evolution. The method uses a novel phylogenetic encoding of copy number data and introduces a point mutation calling method that incorporates CN data and the underlying phylogenetic tree to overcome low-percell coverage in SCWGS. The paper demonstrates CICA on three single-cell data sets, including a novel PDX series, and analyzes the topological properties of the inferred trees. CICA is freely available. This article was authored by Salihi, Sorab, Dory, Fatemay, Churn, Kevin, and others.