This repository contains a literate program for extracting a reconstructed phylogeny from a covasim simulation. Reconstructed phylogenies are used in viral phylodynamics to characterise transmission using viral genomes. This code is intended to provide a bridge between covasim and phylodynamic software.
aezarebski/phylodynamic-covasim
An example of how to use covasim for simulations which can be analysed with phylodynamic methods
PythonMIT