- Discard chatty stdout from santa-sim
- run beast santa-sim and beast on the cluster
Cleanup commentd and eliminate dead code
Change initial population size to one virus.  This still uses a dynamic population, but that will quickly converge on the carrying capacity (== 1000).
make the selectors at least somewhat self-consistent.   It's not ideal, for sure.
Restrict available transmission times to be less than selected donor sample time.
Ignore superfluous files
Checkpoint before experimental excursion
checkpoint divergence analysis before trying to use the precomputed distance measures.
Construct multiple replicates of hiv simulation studies

Vary simulations by population size

Add ipython notebooks for analysis