SIApopr: a computational method to simulate evolutionary branching trees for analysis of tumor clonal evolution

Abstract

Summary: SIApopr (Simulating Infinite-Allele populations) is an R package to simulate time-homogeneous and inhomogeneous stochastic branching processes under a very flexible set of assumptions using the speed of C ++. The software simulates clonal evolution with the emergence of driver and passenger mutations under the infinite-allele assumption. The software is an application of the Gillespie Stochastic Simulation Algorithm expanded to a large number of cell types and scenarios, with the intention of allowing users to easily modify existing models or create their own.

Availability and implementation: SIApopr is available as an R library on Github ( https://github.com/olliemcdonald/siapopr ).

Supplementary information: Supplementary data are available at Bioinformatics online.

Contact: michor@jimmy.harvard.edu.