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Users can freely analyse and visualize genomic variations in heatmaps, phylogenetic trees, haplotype networks, or geographical maps. Sample-specific sequences can be accessed as replaced by detected sequence variations. Conclusions SnpHub can be applied to any species, and we build up a SnpHub portal website for wheat and its progenitors based on published data in recent studies. SnpHub and its tutorial are available at http//guoweilong.github.io/SnpHub/. The wheat-SnpHub-portal website can be accessed at http//wheat.cau.edu.cn/Wheat_Sn