Stephan Schiffels

Population Genetics – Computational Methods - Human History



Teaching Material


All of my software can be found on github. For discussions around MSMC, we have a google group that you can participate in. Most of my recent software is written in Haskell.


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 modified version of MSMC that is still under development. For analysing population size history, MSMC2 is recommended over MSMC. For cross-population analyses I would suggest to wait, since we are still dealing with some issues. 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.


A program to process raw paired-end sequencing data from ancient DNA libraries. Written in Haskell.