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## sstar2 – Archaic Introgression Detection Tool ### Overview sstar2 is a Python software package for detecting introgressed genomic fragments from unsampled or extinct source populations — such as Neanderthals or Denisovans — in modern human genomes (bioRxiv, May 31, 2026). It updates and improves upon the original sstar implementation using quantile regression methods. ### Technical Improvements Over sstar The original sstar tool used generalized additive models to smooth quantile-specific values precomputed from fixed count bins, requiring simulations with fixed numbers of segregating sites. sstar2 replaces this approach with quantile regression to directly estimate S* thresholds at specified null quantiles from simulated genomic windows, removing the fixed-count constraint (bioRxiv, May 31, 2026). ### Significance The S* statistic is widely used in population genetics for detecting archaic introgression — the transfer of genetic material from archaic hominin populations into anatomically modern humans. Improved computational tools for this detection have implications for: - Ancient DNA and paleogenomics research - Understanding human evolutionary history and population structure - Identifying introgressed variants with potential functional significance (e.g., immune genes) ### Strategic Relevance While primarily a research tool, sstar2 is relevant to: - Biotech and genomics companies building population-scale genomics databases - Academic institutions and grant funding in human evolutionary biology - Open-source scientific software development norms and reproducibility standards ### Open Questions - Preprint status; peer review pending - Benchmarking results against original sstar not fully detailed in available abstract