I am working on a big SNP data set from GBS with over 300 individuals from 34 populations. 34 populations compose three closely related species. I tried various assignment tests to see the pop structure but still wanted to see clustering pattern with different approach. Unfortunately, I am not an expert of tree building. For a starter, I am not sure neighbor joining will give me informative inference on relationships among species and populations. Also, there are many heterozygote individuals for many loci since I am using SNPdata set. Which software takes account for ambiguity codes if I do neighbor joining analysis with my SNP data?
Any kind of answers will be very much appreciated.
Thanks in advance.