Software

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.

MSMC

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.

MSMC2

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.

Rarecoal

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.

Tman

This is a tool for running and monitoring large numbers of jobs on Cluster environments. The tool is still in alpha-phase. Written in Haskell.

SequenceTools

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.

MergeAndClip

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