Analysis of amino acid change dynamics reveals SARS-CoV-2 variant emergence

Data and code for paper "Analysis of amino acid change dynamics reveals SARS-CoV-2 variant emergence", now under revision.

The repository contains:

• two files for each of 44 locations (including 19 countries and 25 US states)
  • CoV_<location>_mut5_obs3_absolute.csv (a matrix of amino acid changes [rows], collection weeks [columns], counts of sequences with amino acid change [cells])
  • CoV_<location>_mut5_obs3_totals.csv (a vector of total collected sequences per each week [columns])
• one lineage dictionary (lins_changes75_2_5000_1000.csv)
• one MATLAB script for reproducing all the results of the paper (variants_clustering.m)