In this example, we describe how to perform a codon-based test of positive selection for five alleles from the human HLA-A locus (Nei and Hughes 1991).
The HLA-3Seq.meg" data file, which is used in this tutorial, can be found in the MEGA/Examples folder (The default location for Windows users is C:\Program Files\MEGA\Examples. The default location for Mac users is $HOME/MEGA/Examples, where $HOME is the users home directory).
Computing Synonymous and Non-synonymous Distances
Example 7.1:
Activate the "HLA-3Seq.meg" file. If necessary, refer to Example 1.2 in the MEGA Basics tutorial.
From the main MEGA window launch bar, select Selection | Codon-based Z-Test of Selection.
An Analysis Preferences window appears. For the Model/Method, select the Nei-Gojobori method (Proportion) model.
In the Test Hypothesis (HA: alternative) row, select Positive Selection (HA: dN > dS) from the pull-down menu.
From the Scope row, select the Overall Average option.
For the Gaps/Missing Data Treatment option, select Pairwise Deletion.
Click on "Compute" to accept the default values for the remaining options. A progress indicator appears briefly, and then the computation results are displayed in a results window in grid format.
The column labeled "Prob" contains the probability computed (must be <0.05 for hypothesis rejection at 5% level). The column labeled "Stat" contains the statistic used to compute the probability. The difference in synonymous and non-synonymous substitutions should be significant at the 5% level.
Close the Test of Positive Selection window.