Code and data used to perform the tAI analysis in
deCarvalho, T., Mascolo, E., Caruso, S.M. et al. Simultaneous entry as an adaptation to virulence in a novel satellite-helper system infecting Streptomyces species. ISME J (2023). https://www.nature.com/articles/s41396-023-01548-0
Analysis of the tRNA Adaptation Index (tAI).
The file spa-env.yml can be used to create a conda environment file equipped with all the necessary dependencies for the tAI code.
The code is in the src/tAI folder.
The results can be reproduced by running the tAI_analysis_pipeline.py script.