SIApopr

SIApopr (Simulating Infinite-Allele populations) is a computational method for simulating evolutionary branching trees to analyze clonal evolution in tumors. It is implemented as an R package and uses the C++ language for speed. It is based on the Gillespie Stochastic Simulation Algorithm and allows driver and passenger mutations to emerge under the infinite-allele assumption. Users can modify existing models or create their own.

Topic

Simulation experiment;Computational chemistry;Genetic variation

Detail

  • Operation: Modelling and simulation

  • Software interface: Library

  • Language: R;C++

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: -

  • Credit: The Dana-Farber Cancer Institute Physical Science-Oncology Center.

  • Input: -

  • Output: -

  • Contact: michor@jimmy.harvard.edu

  • Collection: -

  • Maturity: -

Publications

  • SIApopr: a computational method to simulate evolutionary branching trees for analysis of tumor clonal evolution.
  • McDonald TO and Michor F. SIApopr: a computational method to simulate evolutionary branching trees for analysis of tumor clonal evolution. SIApopr: a computational method to simulate evolutionary branching trees for analysis of tumor clonal evolution. 2017; 33:2221-2223. doi: 10.1093/bioinformatics/btx146
  • https://doi.org/10.1093/bioinformatics/btx146
  • PMID: 28334409
  • PMC: PMC5870718

Download and documentation

< Back to DB search