Fig. 2

Simulation trees used to test the SISRS pipeline. All branches for the leftmost trees were initially set to 0.01 substitutions per site. Branch lengths for the center trees (long-deep) were obtained by scaling the leftmost (equal-branch-length) tree to a height of 1, then raising each node height to a power of two, and multiplying by the original tree height [31]. The rightmost (short-deep) tree was obtained similarly, but using a power of one-half. For each of the trees, branch lengths were scaled by multiplying by values from one to six