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:
