Identification of transmission clusters with high influence on shared parameter estimates in Bayesian phylodynamics - the empirics

Scripts and input files for the simulation of phylodynamic trees and sequence alignment as well as Bayesian inference of transmission rates from them; raw data shown in figures of the main text of the manuscript "Identification of transmission clusters with high influence on shared parameter estimates in Bayesian phylodynamics". The analyses of SARS-CoV-2 data are based on 826 sequences and their associated metadata available on GISAID up to January 19th 2025, via gisaid.org/EPI_SET_250119mc and under doi.org/10.55876/gis8.250119mc.