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

Bernasconi, Anna; Mari, Lorenzo; Casagrandi, Renato; Ceri, Stefano

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)

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