Besides simNGS (https://cambridge-ceu.github.io/csd3/systems/setup.html#fn:simngs) earlier, this kickstarts with two modules:
1. selscan
Haplotype based scans for selection, https://cambridge-ceu.github.io/csd3/applications/selscan.html.
2. angsd
Analysis of Next Generation Sequencing Data, https://cambridge-ceu.github.io/csd3/applications/angsd.html.