Releases: theLongLab/CATE
Release list
CATE and Apollo
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
CATE and Apollo
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:
CATE and Apollo
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.
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:
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
CATE and Apollo
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.
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:
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
CATE with Apollo
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
Published RELEASE
This is the first official release after approval of the publication of CATE's complete suite of tools and functions. They have been tested for speed and accuracy.
The pre-built version present in the release should work on most operating systems (Linux/ Unix based) and systems equipped with an Nvidia CUDA-enabled GPU.
Try execution by:
./CATE
You can always perform a build of the project yourself using the following command below on the source code:
nvcc -std=c++17 *.cu *.cpp -o "CATE"
1.0.0.00
RELEASE ONE
This is the first official release of CATE's complete suite of tools and functions. They have been tested for speed and accuracy.
The pre-built version present in the release should work on most operating systems (Linux/ Unix based) and systems equipped with an Nvidia CUDA-enabled GPU.
Try execution by:
./CATE
You can always perform a build of the project yourself using the following command below on the source code:
nvcc -std=c++17 *.cu *.cpp -o "CATE"
0.0.0.03
Pre-release BETA.
All functions are present.
All three neutrality tests at once function has been added.
Tajima's D, Fu and Li, and Fay and Wu tests are fully tested.
The accuracy of other functions in varying queries is yet to be determined.
0.0.0.02
An error in the Mc Donald Kreitman Neutrality Index (NI) test was rectified.
Pre-release BETA.
All functions are present.
Tajima's D is fully tested.
The accuracy of other functions in varying queries is yet to be determined.
0.0.0.01
Pre-release ALPHA.
All functions are present.
Tajima's D is fully tested.
The accuracy of other functions in varying queries is yet to be determined.