Resources for individual-based simulations of viral evolution.
A jupyter notebook exploring simulation frameworks from the perspective of the distribution of fitness effects (DFE) of new mutations. The notebook culminates in an instantiation of a model (from this publication) in which DFE are implicit and free energies of proteins are represented instead.
A python3 script (and associated R visualization script) with a crude DFE together and some sample outputs. Preliminary tests suggest that the recombination model is reasonably effective although the overhead involved in representing genomes is quite high.