CATE's newest release comes complete with Apollo.
Apollo is a comprehensive simulation software for epidemics in a population complete with within-host dynamics. It is powered by CATE, our large-scale parallel processing architecture.
You can cite CATE in your work using:
Perera, D., Reisenhofer, E., Hussein, S., Higgins, E., Huber, C. D., & Long, Q. (2023).
CATE: A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests on large scale genomic data.
Methods in Ecology and Evolution, 00, 1–15.
https://doi.org/10.1111/2041-210X.14168.
Citation of the code can be done via the Zenodo link below:
Apollo is currently available on preprint. If you do use it please cite the preprint:
Apollo: A comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell
Deshan Perera, Evan Li, Frank van der Meer, Tarah Lynch, John Gill, Deirdre L Church, Christian D. Huber, Guido van Marle, Alexander Platt, Quan Long
bioRxiv 2024.10.07.617101; doi: https://doi.org/10.1101/2024.10.07.617101
