A stratified ensemble contains four replicates for each parameter perturbation, one for each for the four possible guide tree permutations.
By default, the permutations have four random number seeds 0, 1, 2 and 3, giving a total of 16 replicates.
This is designed to enable visualization of results such as trees in a 4×4 grid where the guide tree is held fixed on one axis, and HMM parameters are held fixed on the other axis. This shows whether there is systematic error due to the guide tree or to HMM parameters.
