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Table 3 Bacterial genomes used in this paper. All phyla in GenBank as of December 2004 are represented. Bold letters give abbreviations used in Table 1.

From: Automatic selection of representative proteins for bacterial phylogeny

Specific Genome Taxonomy (Phylum; Class)
Corynebacterium glutamicum Actinobacteria;Actinobacteria
Mycob acterium tuberculosis H37Rv Actinobacteria;Actinobacteria
Bifid obacterium longum Actinobacteria;Actinobacteria
Streptomyces avermitilis Actinobacteria;Actinobacteria
Aquifex aeolicus Aquificae;Aquificae
Bac teroides thetaiotaomicron VPI-5482 Bacteroidetes/Chlorobi;Bacteroidetes
Chlor obium tepidum TLS Bacteroidetes/Chlorobi;Chlorobi
Porphyromonas gingivalis W83 Bacteroidetes/Chlorobi;Chlorobi
Chlamydia trachomatis Chlamydiae/Verrucomicrobia;Chlamydiae
Chlamydophila pneumoniae AR39 Chlamydiae/Verrucomicrobia;Chlamydiae
Chloroflexus aurantiacus Chloroflexi;Chloroflexi
Gloeobacter violaceus Cyanobacteria;Chroococcales
Synechococcus sp WH8102 Cyanobacteria;Chroococcales
Syn echocystis PCC6803 Cyanobacteria;Chroococcales
Nos toc sp Cyanobacteria;Nostocales
Pro chlorococcus marinus MIT9313 Cyanobacteria;Prochlorophytes
Deinococcus radiodurans Deinococcus-Thermus;Deinococci
Bacillus subtilis Firmicutes;Bacilli
Oceanobacillus iheyensis Firmicutes;Bacilli
List eria monocytogenes Firmicutes;Bacilli
Staph ylococcus aureus subsp. aureus N315 Firmicutes;Bacilli
Lact ococcus lactis Firmicutes;Bacilli
Strep tococcus pneumoniae R6 Firmicutes;Bacilli
Clost ridium tetani E88 Firmicutes;Clostridia
Thermoanaerobacter tengcongensis Firmicutes;Clostridia
Mycop lasma Firmicutes;Mollicutes
Urea plasma Firmicutes;Mollicutes
Fusobacterium nucleatum Fusobacteria;Fusobacteria
Pirellula sp Planctomycetes;Planctomycetacia
Caul obacter crescentus Proteobacteria;Alphaproteobacteria
Rhodopseudomonas palustris Proteobacteria;Alphaproteobacteria
Bru cella melitensis Proteobacteria;Alphaproteobacteria
Bradyrhizobium japonicum Proteobacteria;Alphaproteobacteria
Mesor hizobium loti Proteobacteria;Alphaproteobacteria
Rick ettsia conorii Proteobacteria;Alphaproteobacteria
Ral stonia solanacearum Proteobacteria;Betaproteobacteria
Neiss eria meningitidis Z2491 Proteobacteria;Betaproteobacteria
Chromobacterium violaceum Proteobacteria;Betaproteobacteria
Bordetella pertussis Proteobacteria;Betaproteobacteria
Nitrosomonas europaea Proteobacteria;Betaproteobacteria
Coxiella burnetii Proteobacteria;Gammaproteobacteria
Esch erichia coli K12 Proteobacteria;Gammaproteobacteria
Haem ophilus influenzae Proteobacteria;Gammaproteobacteria
Pseudomonas aeruginosa Proteobacteria;Gammaproteobacteria
Shigella flexneri 2a Proteobacteria;Gammaproteobacteria
Shewanella oneidensis Proteobacteria;Gammaproteobacteria
Vib rio cholerae Proteobacteria;Gammaproteobacteria
Xanthomonas campestris Proteobacteria;Gammaproteobacteria
Xyl ella fastidiosa Proteobacteria;Gammaproteobacteria
Desulf ovibrio desulfuricans Proteobacteria;delta/epsilon subdivisions
Geo bacter sulfurreducens Proteobacteria;delta/epsilon subdivisions
Campy lobacter jejuni Proteobacteria;delta/epsilon subdivisions
Heli cobacter pylori J99 Proteobacteria;delta/epsilon subdivisions
Wol inella succinogenes Proteobacteria;delta/epsilon subdivisions
Borr elia burgdorferi Spirochaetes;Spirochaetes
Lep tospira interrogans Spirochaetes;Spirochaetes
Trep onema pallidum Spirochaetes;Spirochaetes
Thermotoga maritima Thermotogae;Thermotogae