SmartPCA: Principal Component Analysis to explore population structure and genetic clustering.

ADMIXTURE: Ancestry estimation to reveal admixture patterns and ancestral proportions across individuals.

Signature of Selection: Genome-wide scans (e.g., FST, iHS, XP-EHH) to detect signatures of natural selection and adaptive evolution.

Deliverables:

– High-quality plots (PCA, admixture bar plots, Manhattan plots)

– Annotated tables of significant signature of selection and summary statistics

– Interactive reports (PDF/HTML) summarizing key findings

– Support for group comparisons, temporal analysis, or geographic stratification if metadata is provided