| Abbrev. | Genome | |
|
| Aaeo | Aquifex aeolicus | Bacteria | Aquificales | Aquificaceae | Aquifex |
| Aful | Archaeoglobus fulgidus | Archaea | Euryarchaeota | Archaeoglobales | Archaeoglobaceae |
| Bsub | Bacillus subtilis | Bacteria | Firmicutes | Bacillus/Clostridium group | Bacillus/Staphylococcus group |
| Bbur | Borrelia burgdorferi | Bacteria | Spirochaetales | Spirochaetaceae | Borrelia |
| Cele | Caenorhabditis elegans | Eukaryota | Peloderinae | Rhabditidae | Secernentea |
| Cpne | Chlamydia pneumoniae | Bacteria | Chlamydiales | Chlamydiaceae | Chlamydophila |
| Ctra | Chlamydia trachomatis | Bacteria | Chlamydiales | Chlamydiaceae | Chlamydia |
| Ecol | Escherichia coli | Bacteria | Proteobacteria | gamma subdivision | Enterobacteriaceae |
| Hinf | Haemophilus influenzae Rd | Bacteria | Proteobacteria | gamma subdivision | Pasteurellaceae |
| Hpyl | Helicobacter pylori | Bacteria | Proteobacteria | epsilon subdivision | Helicobacter group |
| Mthe | Methanobacterium thermoautotrophicum | Archaea | Euryarchaeota | Methanobacteriales | Methanobacteriaceae |
| Mjan | Methanococcus jannaschii | Archaea | Euryarchaeota | Methanococcales | Methanococcaceae |
| Mtub | Mycobacterium tuberculosis | Bacteria | Firmicutes | Actinobacteria | Actinobacteridae |
| Mgen | Mycoplasma genitalium | Bacteria | Firmicutes | Bacillus/Clostridium group | Mollicutes |
| Mpne | Mycoplasma pneumoniae | Bacteria | Firmicutes | Bacillus/Clostridium group | Mollicutes |
| Phor | Pyrococcus horikoshii | Archaea | Euryarchaeota | Thermococcales | Thermococcaceae |
| Rpro | Rickettsia prowazekii | Bacteria | Proteobacteria | alpha subdivision | Rickettsiales |
| Scer | Saccharomyces cerevisiae | Eukaryota | Fungi | Ascomycota | Hemiascomycetes |
| Syne | Synechocystis sp. | Bacteria | Cyanobacteria | Chroococcales | Synechocystis |
| Tpal | Treponema pallidum | Bacteria | Spirochaetales | Spirochaetaceae | Treponema |