Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution

Simulated HA sequences

The sequences in this directory represent 90 years of flu HA simulations (1000 bases). The first 200 sites (modulo 3) are “epitope” sites. Richard Neher added functionality to FFPopSim to handle reassortment (that is a defined recombination break point between segments). Modification of default parameters produces roughly flu-like trees. Note that FFPopSim assumes a binary alphabet.