Mutational bias shapes protein evolution across RNA viruses

This repository contains code and data for the analysis of mutational bias impact on amino acid substitution frequencies and amino acid composition in SARS-CoV-2 and other RNA viruses.

Environment

The enviroment contains all the Python dependencies for the analysis. It can be created and activated using the following commands:

mamba env create -f environment.yml -n shift
mamba activate shift

Structure

1. SARS-CoV-2 amino acid substitutions ananlysis
2. RNA viruses mutational spectra derivation and analysis

utils.py contains utility functions for the analysis of amino acid substitutions and mutational spectra.