In this dialog box you can select and view desired options in the Options Summary. Options are organized in logical sections. A lime square in the right cell of a row indicates that you have a choice for that particular attribute. The primary sets of options available in this dialog box are:
Tree Inference
Phylogeny Test and Options
To assess the reliability of a phylogenetic tree, MEGA provides two different types of tests: the Bootstrap test and the Interior branch test. Both of these tests use the bootstrap re-sampling strategy, so you need to enter the number of replicates and a starting random seed. For a given data set, applicable tests and the phylogeny inference method are enabled.
Search Options
This sets the extensiveness of the heuristic search for the Minimum Evolution (ME) tree. MEGA employs the Close-Neighbor-Interchange (CNI) algorithm for finding the ME tree. It is a branch swapping method, which begins with an initial NJ tree.
Include Sites
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 using Complete-deletion option. Alternatively, you may choose to retain all such sites initially, excluding them as necessary using the (Pairwise-deletion option).
Codon Positions
By clicking on the ellipses or the lime square, you may 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.
Labeled Sites
This option is available only if there are labels associated with some or all of the sites in the data. By clicking on the ellipses, you will have the option of including sites with selected labels. If you chose to include only labeled sites, then these sites will be first extracted from the data and 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 in the analysis.
Substitution Model
In this set of options, you can choose various attributes of the substitution models for DNA and protein sequences.
Model
By clicking on the ellipses to the right of the currently selected model, you may select a stochastic model for estimating evolutionary distance (click on the lime square to select this row first). This will reveal a menu containing many different distance methods and models.
Substitutions to Include
Depending on the distance model or method selected, the evolutionary distance can be teased into two or more components. By clicking on the drop-down button (first click on the lime square to select this row), you will be provided with a list of components relevant to the chosen model.
Transition/Transversion Ratio
This option will be visible if the chosen model requires you to provide a value for the Transition/Transversion ratio (R).
Pattern among Lineages
This option becomes available if the selected model has formulas that allow the relaxation of the assumption of homogeneity of substitution patterns among lineages.
Rates among Sites
This option becomes available if the selected distance model has formulas that allow rate variation among sites. If you choose gamma-distributed rates, then the Gamma parameter option becomes visible.