Application of the GS method to protein superfamily data sets obtained from the SCOPe database. Phylogenetic trees of six protein superfamilies were reconstructed using both the GS and NJ|$_{{\rm MSA}\_{\rm p}}$| methods. The red branches of the GS and NJ trees are those supported by large EP (⁠|$\ge $|0.9) and bootstrap (⁠|$\ge $|0.8) values, respectively. The outer circles represent SCOP concise classification strings (functional classes) according to the color legend on each right side (for description, see Supplementary Table S1 available on Dryad). A number in a dotted box indicates an average sequence similarity score of each superfamily proteins. A number below each tree indicates a ratio of interior branches that are supported.