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sstar2

sstar2 is a Python package for S*-based archaic introgression detection with machine learning.

Requirements

sstar2 works on Unix/Linux operating systems and was tested with the following:

  • Python 3.12.13
  • Python packages:
    • black=26.3.1
    • codecov=2.1.13
    • demes=0.2.3
    • flake8=7.3.0
    • msprime=1.4.1
    • numpy=2.4.5
    • onnx=1.19.1
    • onnxruntime=1.26.0
    • pandas=3.0.3
    • pip=26.1.1
    • pydantic=2.12.4
    • pytest=9.0.3
    • pytest-cov=7.1.0
    • scikit-allel=1.3.13
    • scikit-learn=1.8.0
    • scipy=1.17.1
    • skl2onnx=1.19.1

Installation

Users can install sstar2 with pip:

pip install sstar==2.0.0

Users can also use mamba to create a virtual environment and install sstar2 with this build-env.yaml:

mamba env create -f build-env.yaml
conda activate sstar2

Users can also use Apptainer to pull a container image that includes sstar2:

apptainer pull sstar2.sif oras://ghcr.io/xin-huang/sstar:2.0.0

Then run sstar2 with:

apptainer exec sstar2.sif sstar2

Citations

If you find sstar2 is useful, please cite:

  • Koça A, Stöckl A, Chen S, Kuhlwilm M, Huang X. 2026. sstar2: A Python package for S*-based archaic introgression detection with machine learning. bioRxiv: 2026.05.31.729079.
  • Huang X, Kruisz P, Kuhlwilm M. 2022. sstar: A Python package for detecting archaic introgression from population genetic data with S*. Molecular Biology and Evolution 39: msac212.
  • Vernot B, et al. 2016. Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals. Science 352: 235–239.
  • Vernot B, Akey JM. 2014. Resurrecting surviving Neandertal lineages from modern human genomes. Science 343: 1017–1021.
  • Plagnol V, Wall JD. 2006. Possible ancestral structure in human populations. PLoS Genetics. 2: e105.