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.
PCA
Matteo Fumagalli has been working on methods for doing PCA/Covariance based on ANGSD output files.
The main documentation for this is found here: https://github.com/mfumagalli/ngsTools and here https://github.com/mfumagalli/ngsTools#ngscovar