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.