The individual sites in nucleotide or amino acid data can be labeled to construct non-contiguous sets of sites. The Setup Genes and Domains dialog can be used to assign or edit site labels, in addition to specifying them in the input data files. This is shown in the following example of three-sequences in which the sites in the Third Gene are labeled with a + mark. An underscore marks an absence of any labels.
!Gene=FirstGene Domain=Exon1 Property=Coding;
#Human_{Mammal} ATGGTTTCTAGTCAGGTCACCATGATAGGTCTCAAT
#Mouse_{Mammal} ATGGTTTCTAGTCAGGTCACCATGATAGGTCCCAAT
#Chicken_{Aves} ATGGTTTCTAGTCAGCTCACCATGATAGGTCTCAAT
!Gene=SecondGene Domain=AnIntron Property=Noncoding;
#Human ATTCCCAGGGAATTCCCGGGGGGTTTAAGGCCCCTTTAAAGAAAGAT
#Mouse GTAGCGCGCGTCGTCAGAGCTCCCAAGGGTAGCAGTCACAGAAAGAT
#Chicken GTAAAAAAAAAAGTCAGAGCTCCCCCCAATATATATCACAGAAAGAT
!Gene=ThirdGene Domain=Exon2 Property=Coding;
#Human ATCTGCTCTCGAGTACTGATACAAATGACTTCTGCGTACAACTGA
#Mouse ATCTGATCTCGTGTGCTGGTACGAATGATTTCTGCGTTCAACTGA
#Chicken ATCTGCTCTCGAGTACTGCTACCAATGACTTCTGCGTACAACTGA
!Label +++__-+++-a-+++-L-+++-k-+++123+++-_-+++---+++;
Each site can be associated with only one label. A label can be a letter or a number.
For analyses that require codons, MEGA includes only those codons in which all three positions are given the same label. This site labeling system facilitates the analysis of specific sites, as often is required for comparing sequences of regulatory elements, intron-splice sites, and antigen recognition sites in the genes of applications such as the Major Histocompatibility Complex.