In this dialog box, you can select and view options in the Options Summary for the different pattern homogeneity analyses (Composition Distance , Disparity Index, and Disparity Index Test). Options are organized in logical sections and a yellow row indicates that you have a choice for that particular attribute
No. of Monte-Carlo Repetitions
If the Disparity Index Test is selected, MEGA will conduct the Monte-Carlo analysis, for which you need to provide the number of replicates and a starting random seed.
Data Subset to Use
These are options for handling gaps and missing data, including or excluding codon positions, and restricting the analysis to labeled sites (if applicable).
Gaps and Missing Data
You may choose to remove all sites containing alignment gaps and missing information before the calculation begins (Complete-deletion option). Alternatively, you may choose to retain all such sites initially, excluding them as necessary in the pairwise distance estimation (Pairwise-deletion option), or you may use Partial Deletion (Site coverage) as a percentage.
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 and you have selected a nucleotide-by-nucleotide analysis. If they do, you also 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 analysis.
Labeled Sites
This option is available only if some or all of the sites have associated labels. 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.