Hi Mohammad!! The best sofware really is DNAspv5.0 I send link of this pachage for4 download http://www.ub.edu/dnasp/

And link for documentation: http://www.ub.edu/dnasp/DnaSPHelp.pdf

This Software is specialized in molecular markers of mitochondria.

Greetings from Colombia

thanks Richard, but i am working on a plant species ,and i use nuclear marker

No matter, these Sofwate DNAsp got that option!

I f you are using sequences, DNASP is what you need, but if you are using other sorts of genetic markers such as microsatellites, you should use Arlequin

Agree, DNAsp is extremely robust

Thanks