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Genetic code scoring

Whereas the identity scoring scheme considers all amino acid transitions with equal weight, genetic code scoring as introduced by Fitch [4] considers the minimum number of DNA/RNA base changes (0,1,2 or 3) that would be required to interconvert the codons for the two amino acids. The scheme has been used both in the construction of phylogenetic trees and in the determination of homology between protein sequences having similar three dimensional structures [5]. However, today it is rarely the first choice for scoring alignments of protein sequences.