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.
Swapna et al. BMC Evolutionary Biology 2012 12:238 doi:10.1186/1471-2148-12-238