sstar: A Python package for detecting archaic introgression from population genetic data with S*

Xin Huang, Patricia Kruisz, Martin Kuhlwilm

Publications: Contribution to journalArticlePeer Reviewed

Abstract

S* is a widely used statistic for detecting archaic admixture from population genetic data. Previous studies used freezing-archer to apply S*, which is only directly applicable to the specific case of Neanderthal and Denisovan introgression in Papuans. Here, we implemented sstar for a more general purpose. Compared with several tools, including SPrime, SkovHMM, and ArchaicSeeker2.0, for detecting introgressed fragments with simulations, our results suggest that sstar is robust to differences in demographic models, including ghost introgression and two-source introgression. We believe sstar will be a useful tool for detecting introgressed fragments in various scenarios and in non-human species.
Original languageEnglish
Article numbermsac212
JournalMolecular Biology and Evolution
Volume39
Issue number11
DOIs
Publication statusPublished - Nov 2022

Austrian Fields of Science 2012

  • 106013 Genetics
  • 106036 Population genetics
  • 106005 Bioinformatics

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