Selection | Estimate Selection for each Codon (HyPhy)
This option estimates the strength of selection (positive or negative) operating upon each individual codon in an alignment and provides statistical support measures of each estimate. This requires coding DNA sequence data.
For this calculation, MEGA uses a third party program called HyPhy. This is mostly transparent to you (the user). When running the process the progress dialog will have a second tab labeled Command Line Output, this contains the direct output from HyPhy as if you had run it yourself. The first line in the Command Line Output tab contains the actual command which was run for this analysis.