Table 1 Benchmark data for the comparative performance of a translated alignment. Six mammalian protein-coding genes were aligned either as DNA (using ClustalW; default parameters) or via their translations as amino acids (using transAlign; genetic code specified, otherwise default parameters). All analyses used ClustalW v1.83 on an 800-MHz dual-processor Macintosh G4 running OS 10.3.5. The alignment score is taken relative to the corresponding sequence from a manually aligned data set and is the opposite of the Hamming distance (i.e., matching bases score +1, mismatches score +0). The alignment score was calculated for each individual sequence and then averaged over all sequences in each data set. Gene symbols follow the HUGO Gene Nomenclature Committee (HGNC; [21]).

From: transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences