The expected and recovered pectinate topologies. Figure 6A shows the twelve taxon pectinate topology drawn as an unrooted cladogram. 6B show an example where S12 acts as the reference for the NJ Euclidean method, it is 6 steps away according to the symmetric distance from the reference tree in A. C shows another example tree where S12 is the reference but for the parsimony algorithm, and is eight steps away. Both 6B and 6C were evolved at 7.5% average nucleotide substitutions.
Gilbert et al. BMC Genomics 2011 12:456 doi:10.1186/1471-2164-12-456