Is there any reason that dist.genpop cannot be used to calculate pairwise Cavalli-Sforza -Edwardes distances between individauls as follows mygenpop<-genind2genpop(mygenind,pop=mygenind at ind.names) Genmatrix<-dist.genpop(mygenpop,method=2,diag=F,upper=F) cheers Nevil Amos