TreeMix
Description
TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations. In the underlying model, the modern-day populations in a species are related to a common ancestor via a graph of ancestral populations. We use the allele frequencies in the modern populations to infer the structure of this graph. TreeMix uses large numbers of SNPs to estimate the historical relationships among populations, using a graph representation that allows both population splits and migration events.
License
GNU GPL 3
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of treemix and load default version of treemix as
module avail treemix/ # list available modules module load treemix # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail treemix
and choose explicit version you want to use.
Documentation
https://bitbucket.org/nygcresearch/treemix/wiki/Home