Fig. 4
From: Fast algorithms for computing phylogenetic divergence time
Subtree Site Compression Algorithm. The structures supporting the likelihood calculation for a set of three species is shown. At the lower level, the ancestor of the Golden Squirrel and the Groundhog has three unique site combinations shown as three entries in the hash, site lookup and likelihood vectors. The ancestor of all three species has four unique combinations in it’s alignment. The entries in the site lookup table pointing to the descendant of the Golden Squirrel and the Groundhog contain indicies into the likelihood vectors for the descendant