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.
NGSadmix
NGSadmix has it's very own webpage, because we like it so much.
http://www.popgen.dk/software/index.php/NgsAdmix
You can generate input files for NGSadmix easily in ANGSD see Beagle_input.