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An automated method was developed for differentiating closely related <i>B. cereus sensu lato</i> (<i>s.l.</i>) species, especially biopesticide <i>Bacillus thuringiensis,</i> from other human pathogens, <i>B. anthracis</i> and <i>B. cereus sensu stricto</i> (<i>s.s.</i>). In the current research, four typing methods were initially compared, including multi-locus sequence typing (MLST), single-copy core genes phylogenetic analysis (SCCGPA), dispensable genes content pattern analysis (DGCPA) and composition vector tree (CVTree), to analyze the genomic variability of 23 <i>B. thuringiensis</i> strains from <i>aizawai</i>, <i>kurstaki</i>, <i>israelensis</i>, <i>thuringiensis</i> and <i>morrisoni</i> serovars. The CVTree method was the best option to be used for typing <i>B. thuringiensis</i> strains since it proved to be the fastest method, whilst giving high-resolution data about the strains. In addition, CVTree agrees well with ANI-based method, revealing the relationship between <i>B. thuringiensis</i> and other <i>B. cereus s.l.</i> species. Based on these data, an online genome sequence comparison resource was built for <i>Bacillus</i> strains called the <i>Bacillus</i> Typing Bioinformatics Database to facilitate strain identification and characterization.