Dear Zohara,

I recommend to you perform this job with R software:

http://grunwaldlab.github.io/Population_Genetics_in_R/AMOVA.html

Other situation, i.e.:

https://www.researchgate.net/post/How_do_you_compute_and_analyse_AMOVA_with_R_ade4

You can use this software for AMOVA analysis, biology-assets.anu.edu.au/GenAlEx/ 

Thank you very much Jedson Ferreira Cardoso and Kevalkumar Shah

Arlequin is the "classical" program for AMOVA (http://cmpg.unibe.ch/software/arlequin35/).

Thanks Ferruccio Maltagliati 

If you are not familiar with R, use Arlequin

Use ade4, is more friendly than arlequin.

David Gramaje