With this command you can set the options for handling gaps and missing data in the analysis, such as including or excluding codon positions, and restricting the analysis to only some types of labeled sites, if applicable.
Gaps and Missing Data
You may choose to remove all sites containing alignment gaps and missing information before the parsimony analysis begins (Complete-deletion option). Alternatively, you may choose to retain all such sites. In this case, all missing-information and alignment gap sites are treated as missing data in the calculation of tree length. The third option is Partial Deletion (Site coverage) as a percentage of unambiguous data (if there is less unambiguous data than the % specified then it gets deleted).
Codon Positions
Check or uncheck the boxes to select any combination of 1st, 2nd, 3rd, and non-coding positions for analysis. This option is available only if the nucleotide sequences contain protein-coding regions. If it does, you can choose between the analysis of nucleotide sequences or translated protein sequences. If the latter is chosen, MEGA will translate all protein-coding regions into amino acid sequences and conduct the protein sequence parsimony analysis.
Labeled Sites
This option is available only if you have labels associated with some or all of the sites in the data. By clicking on the row, you will be provided with the option of including sites with selected labels. If you choose to include only labeled sites, then these sites will be the first extracted from the data. Then all other options mentioned above will be enforced. Note that labels associated with all three positions in the codon must be included for a full codon to be incorporated in the analysis.