Nadeau et al. 2021 Phylodynamic Analysis Scripts
This repository contains the files necessary to reproduce the Swiss SARS-CoV-2 phylodynamic analyses presented in Nadeau et al. 2021.
In order to run the analyses you will need a machine running either GNU/Linux or MacOS. You will also need to have the following software installed:
- BEAST 2.6 (https://beast2.org/)
- BDMM-Prime (BEAST package, https://github.com/tgvaughan/BDMM-Prime) Version 0.0.24: https://github.com/tgvaughan/BDMM-Prime/releases/tag/v0.0.24
- feast package (BEAST package, https://github.com/tgvaughan/feast)
- R (https://r-project.org)
- tidyverse (R packages, https://tidyverse.org)
- ggdist (R package, https://mjskay.github.io/ggdist/)
Once these are installed, follow the instructions given in the files
CH/README.md (Swiss analyses) and NZ/README.md (NZ analyses) to
reproduce the results.
License
The source code in this repository is made available under the terms of version 3 of the GNU General Public License. A copy of this license can be found in the file named COPYING.