TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data

Bioinformatics. 2016 Jun 15;32(12):1911-3. doi: 10.1093/bioinformatics/btw035. Epub 2016 Feb 9.


Motivation: We introduce TRanslational ONCOlogy (TRONCO), an open-source R package that implements 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 describing 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 evolutionary trajectories of cancer, especially for precision medicine or personalized therapy.

Availability and implementation: TRONCO is released under the GPL license, is hosted at (Software section) and archived also at


Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

  • Algorithms
  • Disease Progression
  • Epigenesis, Genetic
  • Genomics
  • Humans
  • Models, Theoretical*
  • Neoplasms / genetics*
  • Software*
  • User-Computer Interface