Hello and thanks for reading,
I am investigating the population genetic structuring of my study species using whole genome SNP data, and would like suggestions for software that can assign individuals to genetic clusters within my samples. It would also be useful to calculate fixation indeces between sampling sites. In total I have 74 samples from 3 sampling sites, and among these there are just under 20,000 SNPs, though due to low sequencing coverage, some samples have a lot of missing data. There is another complication in that the organism in question undergoes a lot of clonal reproduction, and it's therefore possible that there are genetically identical individuals within my samples, which I suppose will disrupt HWE. I therefore need a program that does not assume HWE (or at that tests for it, at the very least).
Would anyone have any suggestions for what might work best? So far I've played around with adegenet quite a bit, using it to do PCAs, but I'm getting very different results depending on which contigs I use.
I'm new to this and would appreciate recommendations for software that might be suitable for my analyses.