AMOVA on SNP data

Question

[cll92]

Hi,

I have a dataset with snp genotypes (in PLINK format) of individuals of different populations and I would like to perform an AMOVA. I've seen that there is an R package called pegas that provides a function to that:

On the manual it says that I need to provide a model that consists on a distance matrix followed by the stratifications to test. My question is which distance matrix do I need to provide and how can I compute it.

Thanks.