ATGCs are a resource for micro- and macro-evolutionary studies of Bacteria and Archaea - in particular, pan-genomic studies of genes shared across multiple of these closely-related organisms. The major benefit of ATGCs is the large amount of pre-computed data, especially ATGC-COGs, multiple sequence alignments, and pairwise codeML evolutionary measurements. Examples include horizontal gene transfer (e.g., antibiotic resistance), gene neighborhood rearrangements (transposition, prophage integration), synonymous and nonsynonymous codon substitution models, phylogenetic inheritance, and many others
The web page is not pleasant to look at but the data is pre-computed and publicly available. A good starting point for comparative genomics projects.