Figure 2
From: The origins of the evolutionary signal used to predict protein-protein interactions
Schematic of the tree topology comparison method: Alignments of the two proteins under consideration are used to construct the respective trees. TREE-PUZZLE computes the similarities for two trees given the alignment used to construct it. The likelihood scores are compared using likelihood-based statistical tests to ascertain whether both trees explain the data. If they are able to do so, the tree topologies are considered to be similar.