The cophenetic correlation of the Euclidean-based NJ for the Neurospora topology. The distribution of the cophenetic correlations for Tree 3 for 100 replicate Euclidean distance based NJ Trees. Histograms 10A, 10B, and 10C are N. crassa A (NcA) reference based. Histograms 10D, 10E, 10F are N. tetrasperma (tet) reference based. Histograms 10G, 10H, and 10I represent reference taxon N. discreta (disc). Note that the correlations are high, because of the correspondence in branch lengths even though the topologies aren't similar.
Gilbert et al. BMC Genomics 2011 12:456 doi:10.1186/1471-2164-12-456