sstar2: A Python Package for S*-based Archaic Introgression Detection with Machine Learning (opens in new tab)

Detecting introgressed genomic fragments from unsampled or extinct source populations remains challenging. The S* statistic is widely used for this purpose, but the original sstar implementation relies on generalized additive models to smooth quantile-specific values precomputed from fixed count bins, requiring simulations with fixed numbers of segregating sites. Here, we present sstar2, a Python update that replaces this procedure with quantile regression to directly estimate S* thresholds a...