ANGSD: Analysis of next generation Sequencing Data
Latest tar.gz version is (0.938/0.939 on github), see Change_log for changes, and download it here.
Fst PCA
Matteo Fumagalli has been working on methods to estimate Fst and doing PCA based on ANGSD output files.
Fst
- Generate .sfs files from each population using ANGSD RealSFS