Individual-based simulations of viral evolution.
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.ipynb_checkpoints
lundy_phage
DFEM_py_nb.ipynb
DFEM_slides.ipynb
DFEM_slides.slides.html
README.md

README.md

Simulations

Resources for individual-based simulations of viral evolution.

DFEM_py_nb.ipynb

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.

lundy_phage

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.