Luca De Sano, Giulio Caravagna, Daniele Ramazzotti, Alex Graudenzi, Giancarlo Mauri, Bud Mishra and
Marco Antoniotti

Motivation: We introduce TRanslational ONCOlogy (TRONCO), an open-source R package that im- plements the state-of-the-art algorithms for the inference of cancer progression models from (epi)genomic mutational profiles. TRONCO can be used to extract population-level models describ- ing the trends of accumulation of alterations in a cohort of cross-sectional samples, e.g. retrieved from publicly available databases, and individual-level models that reveal the clonal evolutionary history in single cancer patients, when multiple samples, e.g. multiple biopsies or single-cell sequencing data, are available. The resulting models can provide key hints for uncovering the evo- lutionary trajectories of cancer, especially for precision medicine or personalized therapy. Availability and implementation: TRONCO is released under the GPL license, is hosted at http:// bimib.disco.unimib.it/ (Software section) and archived also at bioconductor.org.

Contact: tronco@disco.unimib.it