African yam bean DArTseq diversity panel — analysis pipeline (version 0.1.0)

End-to-end reproducible analysis pipeline for a 95-line Sphenostylis stenocarpa DArTseq diversity panel with 13 seed-quality and morphometric phenotypes, anchored to the chromosome-scale S. stenocarpa reference (Shorinola et al. 2024). Covers QC, PCA, ADMIXTURE, AMOVA, Weir-Cockerham F_ST, LD decay, F_IS, ML phylogenies (IQ-TREE and RAxML-NG), mixed-model GWAS, GBLUP genomic prediction, Daetwyler ceiling, candidate-gene callouts against the Funannotate annotation, locus-zoom views with Haploview-style triangular LD heatmaps, runs of homozygosity, and topGO GO-term enrichment. Includes the canonical Paper 1 figure set (52 figures) and table set (9 tables) under results/04_publication_plots/. Author list under .creators is the code-side primary author. Manuscript co-authorship (Prof. B.D. Adewale and collaborators) will be added on manuscript publication.