Besides R/rehh and simNGS (https://cambridge-ceu.github.io/csd3/systems/setup.html#fn:simngs) earlier, this kickstarts with these modules:
- selscan. Haplotype based scans for selection, https://cambridge-ceu.github.io/csd3/applications/selscan.html.
- angsd. Analysis of Next Generation Sequencing Data, https://cambridge-ceu.github.io/csd3/applications/angsd.html.
- Relate. Software to estimate genome-wide genealogies for thousands of samples, https://cambridge-ceu.github.io/csd3/applications/relate.html
- CLUES2. A method for inferring and evaluating evidence for selection, https://cambridge-ceu.github.io/csd3/applications/clues2.html.
- fastsimcoal2. Fast sequential Markov coalescent simulation of genomic data under complex evolutionary models, https://cambridge-ceu.github.io/csd3/applications/fsc2.html.
- hapstat. haplotype-disease association, https://cambridge-ceu.github.io/csd3/applications/hapstat.html.
- CCphylo. a software suite designed to easen phylogenetic analysis, https://cambridge-ceu.github.io/csd3/systems/setup.html#fn:ccphylo.