funny, this question has been discussed not a week ago (something like "software for PCA and PCoA to analyze genetic structure") but for the life of me I cannot find it using the RG search engine (it seems to have a really weird indexing system). 

Anyway, there are several excellent R packages for PCA-related analysis of any sort of multivariate data, including genetic, most notably the package vegan. Assuming we need to analyze genetic distances, there is vegdist function and pcoa (package ape) to perform principal coordinate analysis (same as metric multidimensional scaling). Plot it with polygons and 95%-confidence ellipses using functions ordihull and ordiellipse, and if you want to run permutation-based anova on this, use function adonis.  Package adegenet has a very cool series of functions for discriminant analysis of principal components, with the main function dapc. 

The best software is maybe the more used in the scientific community, and with more articles of high level published

for a beginner i would suggest free software available STRUCTURE, GEN ALEX ARLEQUEN. However for STRUCTURE population should be under random association of alleles. hope this helps. for advanced person can go for JMP, SAS, R