Stephan Schiffels

Population Genetics – Computational Methods - Human History



Teaching Material

Disclaimer: These courses are currently not designed to “just work” if you run them at home. They are dependent on data that I provided to workshop participants at the time, and specific softare to be installed. Nevertheless, they may provide useful resources for some readers even outside of the original teaching context, that’s why I’m posting them here.


All of my software can be found on github. For issues and discussions, please use the respective issues tracker, for example here for questions related to MSMC2.


Poseidon is a large initiative that is under development. We are preparing a public release soon


A method for analysing multiple genome sequences to infer past population sizes and separation history between populations. A utilities framework msmc-tools is available as well. Written in D and python.


A method to model population graphs from the rare site frequency spectrum in multiple populations with large numbers of samples. A utilities package rarecoal-tools is available as well. Written in Haskell.


This package contains two programs “pileupCaller” and “vcf2eigenstrat”. PileupCaller is used to sample alleles from an alignment file at a set of positions. VCF2eigenstrat converts a VCF file into eigenstrat format. Written in Haskell.