The notebooks here contain the steps taken to compute -

1. Population structure - PCA & K-means clustering
2. Linkage disequillibrium - SNP based & Whole genome window based
3. Genetic Differentiation - Hudson FST across clusters
4. Genetic Diversity - Tajima’s D, Theta pi & Theta watterson
5. Haplotype Diversity - moving window genome wide
6. Selection scans & ¡HS score

Tools used include scikit-allel library (version - 1.3.13), ADMIXTURE (version - 1.3.0), and custom python code, with all results reproducible and visualized for interpretation.