I suggest you PGDSpider (just google it for downloading) to convert all types of genotyping data into any other kind of format used for classical genetic analyses. It is super convenient! Cheers

Thank you Tommy. I use PDGspider but I need understand how to create the matrix for this specific analyze.

thank you!

hi dear Laia Juliana Muñoz

as you know, mantel test compare two same rank matrix,

so first, you should create the matrices then compare together.

if you want to create a dendrogram must compare the similarity/dis-similarity matrices and cophenetic matrices.

Hi Mostafa thank you. Yes I need to create the matrix but I dont find how I can to estimate the matrix values. FSTAT doesnt have manual for to create a matrix 

dear Laia Juliana Muñoz,

this link can be useful

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-4-29

http://www.angelfire.com/nj2/arabidopsis/MatGAT.html