I was wondering if there was a package that helps with RAPD data, specifically population genetics. I heard about "poppr" but I am not sure if it works for this type of marker, it says it works for dominant data but it never specifies.
Poppr should work for your needs. There are other packages you may want to explore as well though; 'PopGenome', 'Pegas', and 'Adegenet' depending on your needs. A bit more explanation might help narrow it down.