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


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


BACKGROUND
Supplementary data are available at Bioinformatics online.


BACKGROUND
michor@jimmy.harvard.edu.
Department of Biostatistics and Computational Biology, Center for Cancer Evolution, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.
Thomas O
TO
McDonald
Department of Biostatistics and Computational Biology, Center for Cancer Evolution, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.
Franziska
F
Michor
D000465:Algorithms; D060965:Clonal Evolution; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D006801:Humans; D009369:Neoplasms / Q000235:genetics / Q000503:physiopathology*; D012984:Software; D013269:Stochastic Processes