HGTree database provides genome-wide horizontal gene transfer information for 2,472 completely sequenced prokaryotic genomes (156 Archaea and 2,316 Bacteria). HGTree defines lateral gene transfer by comparing the gene tree for each orthologous gene set to the reference species tree. Conflict between gene and species trees is taken as indication of non-vertical evolution (including HGT and convergence) and is displayed graphically for quick understanding.