This repository contains R and Python scripts utilized in the manuscript Komissarov et al., 2021

All necessary data files required to reproduce the results are provided in the data folder.

Scripts in python are required for tree manipulations and visualization.

get_lineages_and_dates.py allows to find all Russian lineages on the tree and visualize them.

get_singletons.py and get_stem_clusters.py allow to find Russian singletons and stem clusters.

For clade definitions see Figure 4

R scripts Figure1_draw_maps.R and Figure6_Lineages_stem_times.R are required to construct Figures 1 and 6 from the manuscript.