I recently published AdmixPy on GitHub, a fast implementation of f-statistics, qpAdm, and qpWave in Python that runs on Linux, macOS, and Windows. It works directly on the new AADR TGENO distribution format and is faster than ADMIXTOOLS 2 on equivalent workloads. Supported input formats: EIGENSTRAT (.geno/.snp/.ind), packed AncestryMap (.geno/.snp/.ind), TGENO (.tgeno/.snp/.ind), and SNP-major PLINK binary (.bed/.bim/.fam).

Setup

AdmixPy requires Python 3.10 or newer and runs on Linux, macOS, and Windows. You’ll also need git to clone the repository.

Clone the repository and enter it:

git clone https://github.com/system0x7/admixpy.git
cd admixpy

Create and activate a virtual environment:

python3 -m venv venv
source venv/bin/activate

On Windows, activate with venv\Scripts\activate instead.

Install the package:

python -m pip install --upgrade pip
python -m pip install -e .

Verify the install:

python -c "import admixpy; print(admixpy.__file__)"

You should see a path ending in admixpy/__init__.py. If you get an ImportError, double-check that the virtual environment is activated.

Usage

The convenience wrappers map directly to the methods you’d expect:

admixpy.f2(data, pop1, pop2)
admixpy.fst(data, pop1, pop2) 
admixpy.f3(data, pop1, pop2, pop3)
admixpy.f4(data, pop1, pop2, pop3, pop4)
admixpy.qpwave(data, left, right)
admixpy.qpadm(data, target, left, right)

data can be a genotype dataset prefix or precomputed f2 data. For PLINK input, population labels are read from the FID column of the .fam file.

Start a Python REPL in the directory containing your AADR files and run an f4 statistic:

>>> import admixpy as a
>>> prefix = "v66_compatibility"
>>> a.f4(prefix, "Chimp", "Turkey_N", "Sardinian", "French")

Result:

Loading f2 data for 4 population pairs
Reading TGENO data: 1243531 SNPs, 23259 samples, 131 selected samples, 4 populations
Detecting pseudohaploid samples from first 1000 SNPs
Reading TGENO sample 131/131      
Filtering SNPs
Computing f2 block 708/708: SNP rows 569568-569807      
Computing f4 for 1 population combinations
    pop1      pop2       pop3    pop4       est        se     z    p
0  Chimp  Turkey_N  Sardinian  French -0.001644  0.000109 -15.1  0.0

The significantly negative (Z=−15.1Z=-15.1) estimate with AA as outgroup indicates that Anatolian Neolithic farmers share more drift with Sardinians than with French, reflecting the stronger Neolithic Farmer affinity in Sardinia. Follow-up posts will work through f-statistics, qpAdm and qpWave models on AADR data using AdmixPy.