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selection-statistics

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Scans genomes for natural selection with SFS tests (Tajima's D, Fay & Wu H, Zeng E, SweepFinder2 CLR), haplotype tests (iHS, nSL, XP-EHH, Rsb, H12), and differentiation (FST, PBS) using scikit-allel, selscan, and SweepFinder2. No single statistic separates selection from demography at one locus, so the deliverable is empirical genome-wide outliers plus multiple orthogonal signals, not an absolute cutoff. iHS detects incomplete sweeps and collapses to zero at fixation while XP-EHH catches fixed sweeps; iHS/nSL standardize within derived-allele-frequency bins but XP-EHH gets a genome-wide z-score; derived-allele tests need substitution-model polarization; background selection mimics FST and CLR. Use when computing selection statistics like FST, Tajima's D, iHS, or XP-EHH, or scanning for selective sweeps. For phasing inputs see phasing-imputation/haplotype-phasing; for dN/dS see comparative-genomics/positive-selection.

When to use

• computing selection statistics like FST, Tajima's D, iHS, or XP-EHH
• scanning for selective sweeps
• SFS neutrality tests
• haplotype/EHH sweep statistics
• differentiation outliers (FST, PBS)
• CLR scans
• polygenic Qx
• standardization and demography-aware outlier interpretation

When not to use

• PCA/ADMIXTURE population assignment
• LD/EHH mechanics
• scikit-allel array-API mechanics
• phasing
• dN/dS and McDonald-Kreitman

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