## Simulation

Model source code can be found in the antigen repository. The exact code to produce these simulations is antigen.jar. This requires Java 1.7 to compile and running the simulation with 45 million hosts requires a lot of memory. To run, navigate to a directory with `parameters.yml`

and type:

```
java -Xmx22G -jar ../../antigen.jar Antigen
```

This will load in the `parameters.yml`

and output `out.branches`

, `out.summary`

, `out.timeseries`

, `out.tips`

and `out.trees`

. Estimation of summary statistics (like migration rate) requires additional post-processing. The file `out.stats`

is computed by running the Mathematica notebook `scripts/antigen-analysis.nb`

.

The summary figure is created from the entire set of `out.stats`

files by the Mathematica notebook `scripts/summary.nb`

.

Model are parameterized with 3 demes and 2 age compartments: