I am analyzing data for diversity studies. I have 70 individuals. Now the result of STRUCTURE divides this into 3 sub-population based on band scoring (1 and 0). Now my question is do I define 3 sub-population while calculating diversity parameters such as NEI, F and Gst? or should I just use 70 individuals as an input without defining sub-population?
I am using DARWIN and GENAIex.
Please clear up my confusion and also if you have any suggestion for better software (user-friendly) which can do all these analysis easily?