Analysis Preferences (Estimate Selection for each Codon)

In this dialog box, you can view and select desired settings for options which are listed in the Options Summary tab. Available options are organized into logical sections. A yellow row indicates an analysis option for which there are multiple settings available. To view the available settings for an option, click on its row. The three primary categories of options available for analysis are:

Tree to Use

MEGA requires a tree to start the analysis. This tree can either be provided by a user or automatically generated by HyPhy. If you wish to specify a tree, change the value of this option to Specify a tree from a file or Use Topology Editor. If you are specifying a tree from a file, another option User Tree File will become enabled.

User Tree File

This option contains the path to a tree file you would like to use for this analysis. This option is only on when Tree to Use is set to Specify a tree form a file. To choose a file click on the row once and you will see an ellipsis button [], click it.

Substitution Model

In this set of options, you can select various attributes of the substitution models for DNA and AA sequences.

Substitutions Type

For this analysis, only the Syn-Nonsynonymous option is available.

Model/Method

Here you can select a stochastic model for estimating evolutionary distance by clicking on the row then selecting from one of the models that are applicable for the currently selected Substitutions Type.

In this particular analysis there are only 4 models available (Felstein 1981, Hasegawa-Kishino-Yano, Tamura-Nei, and General Time Reversable). These are the models supported by HyPhy which MEGA uses as its calculation engine for this particular analysis.

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/Missing Data Treatment

For this analysis setting, 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 or you may use Partial-Deletion (Site Coverage Cutoff ) as a percentage.