CATE's newest release comes complete with Apollo.
Apollo is a comprehensive simulation software for epidemics in a population, complete with within-host dynamics. CATE, our large-scale parallel processing architecture, powers it.
Apollo has been published in Nature Communications. If you do use it, please cite the journal article:
Perera, D., Li, E., Gordon, P.M., van der Meer, F., Lynch, T., Gill, J., Church, D.L., de Koning, A.P.J., Huber, C.D., van Marle, G., Platt, A., Long, Q., 2025.
Apollo: a comprehensive GPU-powered within-host simulator for viral evolution and infection dynamics across population, tissue, and cell.
Nature Communications 2025 16:1 16, 1–17.
https://doi.org/10.1038/s41467-025-60988-8
A detailed user manual describing how to use CATE is provided below:
Apollo also comes with a video tutorial, you can either download and watch using the GitHub repo's version or watch online via Vimeo:. The links to both are below:
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 with Apollo can be done via the Zenodo link below:
This release comes with minor bug fixes