AdmixTools: qpgraph, qp3Pop (f_3 test), qpBound, qpDstat, qpF4ratio, rollof

AdmixTools

Install admixtools
You can do it with git (you have to have it installed):

sudo apt-get install git
git clone https://github.com/DReichLab/AdmixTools.git

(you can add at the end the folder where you want it downloaded).
There you have the AdmixTools folder.

Another option, if you don’t like git, is wget (or just download the zip directly):

wget https://github.com/DReichLab/AdmixTools/archive/master.zip
unzip master.zip

And there you have the AdmixTools-master folder.

It has to be installed from source, and I had the following packages installed – however, probably just the basic packages (GSL, lapack and openblas, in bold) would have been enough, as stated in the software instructions (I would install at least those in bold):

sudo apt-get install gsl-bin libgsl-dbg libgsl-dev
(you might need to install libgsl0-dbg and libgsl0-dev instead)

sudo apt-get install gfortran liblapack3 liblapack-dev liblapack-doc liblapack-pic liblapacke liblapacke-dev

sudo apt-get install libblas3 libblas-common libblas-dev libblas-doc libatlas3-base libatlas-base-dev libblas-test libopenblas-base libopenblas-dev

To install (per the instructions in the README file), from the /src/ folder:

cd AdmixTools/src
make clobber
make install

If you encounter some strange problems, follow the instructions of the README:

wget https://reich.hms.harvard.edu/sites/reich.hms.harvard.edu/files/inline-files/AdmixTools_Example_Data.tar_.gz
tar -zxvf AdmixTools_Example_Data.tar_.gz

The extracted folder /data/ should be in the AdmixTools/ or AdmixTools-master/ folder. Now from the /examples/ folder run the examples:

cd AdmixTools/examples
./mklog

If you encounter problems, it is probably related to your system.

Using ADMIXTOOLS

I have not used these tools myself. The documentation seems pretty straightforward – at least if you are able to use other instructions, like those for PCA and ADMIXTURE.

Useful instructions from other websites:

Samples

Samples used in the Indo-European demic diffusion model:

genetic-history-europe-eurasia
Tentative sketch modelling the genetic history of Europe and West Eurasia from ancient populations up to the Neolithic, according to results in recent Genetic papers and archaeological models of known migrations.

Other samples included in the model, from recent genetic papers:

european-hunter-gatherer
Structure and population change in European populations with mainly hunter gatherer ancestry, modified from Mathieson et al. (2017).
middle-east-farmer-ancestry-europe
Structure and population change in European populations with Middle Eastern farmer ancestry, modified from Mathieson et al. (2017).
steppe-bell-beaker
Steppe ancestry in Bell Beaker, modified from Olalde et al. (2017)

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