Use build_TreeSim.sh to use TreeSim_2.4.tar.gz to access the sim.rateshift.age function for simulating trees.

The simulate_trees.R produces 200 trees with one skyline interval (so uses constant rates for simulations).

templates/ssRanges_inference_template_one_int.xml provides the basic XML used to generate analysis files for each simulated tree.

The rates used in each simulation is saved in true_rates.csv. The trees are saved in simulated_trees/200_trees.out.

For each tree index from 0 to 199, there is a subfolder in inf which contains the generated XML, and resulting log and tree files.

The XML files are run using slurm-inferences.sh. ssr.jar is used to access the ssRanges BEAST2 package.