Current Release

  • November 16, 2015
New Features:
  • Better estimation of the population tree when no outgroup is specified, or when the --keep-outgroup option is used. This for example allows running hapflk on datasets with only two populations and no outgroup available.
  • Estimation of the population tree and kinship matrix no longer depends on R being installed.

System requirements

We provide a source package to compile hapflk. To build, you will need python version >=2.7, the numpy and scipy packages and a C compiler installed on your system. Then

Unpack the archive (tar -xvzf hapflk-version.tar.gz)
cd in the directory created and issue the command:
sudo python install

If you use hapflk to estimate the population tree, you will need R and the ape and phangorn packages installed on your system. No longer needed starting with version 1.3


List of Command line options

Tutorial: Hapmap data and the LCT gene

Building local population trees to pinpoint selected populations

Release History


For bug reports and feature requests, please send an email to bertrand.servin at Thanks.