Intra-tumor heterogeneity (ITH) has been a major confounding factor in cancer prognosis, treatment, and prevention [1–4]. ITH describes the phenomenon in cancer when one tumor contains multiple subclones, each characterized by a certain group of mutations [2]. When ITH is not fully characterized, cancer treatment tends to target only major clones whereas the small subclones may grow mid- or post-treatment, leading to cancer relapse [5–7]. Fully characterizing ITH helps understanding cancer growth and thus can improve cancer treatment and prevention [1, 8–13]. To achieve that, one needs to correctly detect mutations in each cell and infer the phylogenetic tree of the subclones.
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