jupyter notebook code for analyses found in the scripts subdirectory. Input and output data found in the data subdirectory.
see environment.yml file
The structural context of mutations in proteins predicts their effect on antibiotic resistance
Anna G. Green, Mahbuba Tasmin, Roger Vargas Jr, Maha R. Farhat
bioRxiv 2025.09.23.676583
Code to generate the structure database is found here and is a fork from the EVcouplings repository.
This study uses ancestral sequence reconstruction data originally published in Vargas et al., PNAS, 2023.