gpps: An ILP-based approach for inferring cancer progression with mutation losses from single cell data
Motivation: In recent years, the well-known Infinite Sites Assumption (ISA) has been a fundamental feature of computational methods devised for reconstructing tumor phylogenies and inferring cancer progression where mutations are accumulated through histories. However, some recent studies leveraging Single Cell Sequencing (SCS) techniques have shown evidence of mutation losses in several tumor samples [Kuipers et al., 2017], making the inference problem harder. Results: We present a new tool, gpps, that reconstructs a tumor phylogeny from single cell data, allowing each mutation to be lost at most a fixed number of times. Availability: The General Parsimony Phylogeny from Single cell (gpps) tool is open source and available at https://github.com/AlgoLab/gppf.
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