In this dialog box you can select and view the desired options in the Options Summary. Options are organized in logical sections. A yellow row indicates that you have a choice regarding the attribute in that row. The three primary sets of options available in this dialog box are:
Analysis
Variance Estimation Method
Use this to specify whether to compute Distances only or Distances and Standard Errors using the selected estimation method. If you select the latter, then you are given a choice as to how to compute it in the No. of Bootstrap Replications box.
When you compute average distance or diversity, only the bootstrap method is available for computing standard errors.
Substitution Model
In this set of options, you choose the various attributes of the substitution models.
Substitutions Type
Here you may select a substitutions type of Nucleotide, Syn-Nonsynonymous, or Amino Acid. The selection in this row effects the available models in the model row.
Model
Here you select a stochastic model for estimating evolutionary distance by clicking on the row then selecting a model for the current Substitutions Type.
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 row, you will be provided with a list of components relevant to the chosen model.
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.
Data Subset to Use
These are options for handling gaps or 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 for 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.
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.