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.
MsToGlf
For the Korneliussen2013 paper, we simulated data according to genotypes simulated from ms/msms output. For this we used the msToGlf program found in the 'misc/' subfolder of the angsd tar ball.