I am new to the plink SNPs data (genotypes) as I am used to work with markers.
I am wondering if there are any packages that can analyze basic pop gen parameters in SNP data such as DNASP and GenAlEx which are for microsatallite (sequences) data.
Specifically, I am interested in calculating Waterson's theta, FIS,FIT, FST, AMOVA, Tajima's D,and the nucleotide diversity (pi). I know I can calculate these quantities in DNASP. Is there something corresponding to DNASP for SNP data.
I would really appreciate you guidance and suggestions with this.