Sequences are compared codon A codon is triplet of nucleotides that codes for a specific amino acid.-by-codon A codon is triplet of nucleotides that codes for a specific amino acid.. These distances can only be computed for protein-coding sequences or domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog..