MutAntiGen

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Input file:

There is one main control file, 'parameters_load.yml', that contains all the simulation parameters. The annotation describes what each parameter is or does.

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Running:

From the command line, you can run the code like this:
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java -Xmx 2G -jar Antigen.jar

Make sure you are in the Antigen directory though or Java will not be able to find the 'parameters_load.yml' input file.

The -Xmx argument tells Java how much memory to allocate before you launch the program. For population sizes of 40 million and running the sims with 40 years of antigenic evolution, I was using 48G of memory.

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Output:

All the output is written to files beginning with 'out.':

out.antigenicDistance <-- contains the antigenic distance matrix for all antigenic types in the tree
out.antigenicSamples <-- the number of samples belonging to each antigenic type over time which is used to reconstruct the time series of antigenic dynamics
out.branches <-- info about the branches in the tree (not used by me)
our.mrcaSeries <-- contains the time of the MRCA in the tree over time
out.mutationSeries <-- contains the population mutation load distribution over time
out.simmapAntigenic <-- the SimMap tree with annotation for the antigenic type of the lineages in the tree
out.simmapLoad <-- the SimMap tree with annotation for the mutational load of the lineages in the tree
out.summary <-- summary of simulation (not used by me)
out.timeseries <-- time series of the population dynamics
out.tips <-- info about the tips in the tree (not used by me)
out.trees <-- the tree in newick format
out.trunkAntigenicShifts <-- the sizes of the antigenic transitions occurring along the trunk \fs24




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