I really want to know how to analysis and get the genetic divergence in intrapopulations and intergeneric populations in details with all steps followed in MEGA and other softwares.
Load your aligned sequences in the appropriate format then go to the Compute Pairwise Distance tab. In there, you will have a number of options to toggle. I find that the missing data option can have a significant effect on the results. Consult the manual to see which option suits your data.