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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 setup.py 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