Figure 1: Phylogenetic Trees of Different Types of Proteases: Phylogenetic trees of different proteases were built from sequence analysis(a) and structure analyses including backbone dihedral angle structure alignment method(b,c) and TM-align (d). Sequence alignment generated rather obscure clustering between serine-type proteases (yellow dots) and metalloproteases (purple dots). Aspartic-type proteases and cysteine-type proteases were dotted with cyan and red color each. Trees with our new approach showed better clustering than that of seqeunce method as explained in the text. logPr tree showed slightly better clustering than RamRMSD tree, showing weight imposition on closer similarity can improve errors of RMSD. Our two trees(b,c) showed comparable accuracy of clustering with the tree from TM-score of TM-align(d).