This repository contains a simple Jupyter notebook written by Jesse Bloom that makes plots of spike amino-acid mutations in different SARS-CoV-2 Pango clades like this one:
Note that when you make the plots there is an option at the bottom of the plot to show all differences from Wuhan-Hu-1 among the clades as above, or you can just show sites that differ among the clades like below:
The notebook reads the information on Pango clade definitions from Cornelius Roemer's definitions at https://github.com/corneliusroemer/pango-sequences. Note that it shows substitutions and deletions, but not insertions.
If you just want to input a custom set of clades and make the plot without cloning this repo yourself, use the interactive notebook at https://mybinder.org/v2/gh/jbloom/SARS2-clade-spike-diffs/main?labpath=spike-diffs.ipynb (this make take a minute to load).
Otherwise, install JupyterLab as well as the packages in requirements.txt, open JupyterLab, and run the notebook spike-diffs.ipynb.