#NEXUS [!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file. Generated on May 17, 2024; 2:09 GMT TreeBASE (cc) 1994-2008 Study reference: Wu D., Hugenholtz P., Mavromatis K., Pukall R., Dalin E., Ivanova N.N., Kunin V., Goodwin L., Wu M., Tindall B.J., Hooper S.D., Pati A., Lykidis A., Spring S., Anderson I.J., D’haeseleer P., Zemla A., Singer M., Lapidus A., Nolan M., Copeland A., Chen F., Cheng J., Lucas S., Kerfeld C., Lang E., Gronow S., Chain P., Bruce D., Rubin E.M., Kyrpides N.C., Klenk H., & Eisen J.A. 2009. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature, 462(7276): 1056-1060. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S10965] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=720; TAXLABELS Acaryochloris_marina_MBIC11017 Acholeplasma_laidlawii_PG_8A Acidimicrobium_ferrooxidans Acidiphilium_cryptum_JF_5 Acidobacteria_bacterium_Ellin345 Acidothermus_cellulolyticus_11B Acidovorax_avenae_subsp._citrulli_AAC00_1 Acidovorax_sp._JS42 Acinetobacter_baumannii_ACICU Acinetobacter_baumannii_ATCC_17978 Acinetobacter_baumannii_AYE Acinetobacter_baumannii_SDF Acinetobacter_sp._ADP1 Actinobacillus_pleuropneumoniae_L20 Actinobacillus_pleuropneumoniae_serovar_3_str._JL03 Actinobacillus_pleuropneumoniae_serovar_7_str._AP76 Actinobacillus_succinogenes_130Z Actinosynnema_mirum Aeromonas_hydrophila_subsp._hydrophila_ATCC_7966 Aeromonas_salmonicida_subsp._salmonicida_A449 Agrobacterium_tumefaciens_str._C58 Akkermansia_muciniphila_ATCC_BAA_835 Alcanivorax_borkumensis_SK2 Alicyclobacillus_acidocaldarius Alkalilimnicola_ehrlichei_MLHE_1 Alkaliphilus_metalliredigenes_QYMF Alkaliphilus_oremlandii_OhILAs Anabaena_variabilis_ATCC_29413 Anaerococcus_prevotii Anaeromyxobacter_dehalogenans_2CP_C 'Anaeromyxobacter sp. Fw109-5' Anaplasma_marginale_str._St_Maries Anaplasma_phagocytophilum_HZ Aquifex_aeolicus_VF5 Arcobacter_butzleri_RM4018 Arthrobacter_aurescens_TC1 Arthrobacter_sp._FB24 'Aster yellows witches''-broom phytoplasma AYWB' Atopobium_parvulum Azoarcus_sp._BH72 Azoarcus_sp._EbN1 Azorhizobium_caulinodans_ORS_571 Bacillus_amyloliquefaciens_FZB42 Bacillus_anthracis_str._Ames Bacillus_anthracis_str._Ames_Ancestor Bacillus_anthracis_str._Sterne Bacillus_cereus_ATCC_10987 Bacillus_cereus_ATCC_14579 Bacillus_cereus_E33L Bacillus_cereus_subsp._cytotoxis_NVH_391_98 Bacillus_clausii_KSM_K16 Bacillus_halodurans_C_125 Bacillus_licheniformis_ATCC_14580 Bacillus_pumilus_SAFR_032 Bacillus_subtilis_subsp._subtilis_str._168 'Bacillus thuringiensis serovar konkukian str. 97-27' Bacillus_thuringiensis_str._Al_Hakam Bacillus_weihenstephanensis_KBAB4 Bacteroides_fragilis_NCTC_9343 Bacteroides_fragilis_YCH46 Bacteroides_thetaiotaomicron_VPI_5482 Bacteroides_vulgatus_ATCC_8482 Bartonella_bacilliformis_KC583 Bartonella_henselae_str._Houston_1 Bartonella_quintana_str._Toulouse Bartonella_tribocorum_CIP_105476 Baumannia_cicadellinicola_str._Hc_Homalodisca_coagulata Bdellovibrio_bacteriovorus_HD100 Beijerinckia_indica_subsp._indica_ATCC_9039 Beutenbergia_cavernae Bifidobacterium_adolescentis_ATCC_15703 Bifidobacterium_longum_DJO10A Bifidobacterium_longum_NCC2705 Bordetella_avium_197N Bordetella_bronchiseptica_RB50 Bordetella_parapertussis_12822 Bordetella_pertussis_Tohama_I Bordetella_petrii_DSM_12804 Borrelia_afzelii_PKo Borrelia_burgdorferi_B31 Borrelia_garinii_PBi Borrelia_hermsii_DAH Brachybacterium_faecium Brachyspira_murdochii Bradyrhizobium_japonicum_USDA_110 Bradyrhizobium_sp._BTAi1 Bradyrhizobium_sp._ORS278 Brucella_abortus_S19 'Brucella abortus biovar 1 str. 9-941' Brucella_canis_ATCC_23365 Brucella_melitensis_16M Brucella_melitensis_biovar_Abortus_2308 Brucella_ovis_ATCC_25840 Brucella_suis_1330 Brucella_suis_ATCC_23445 Buchnera_aphidicola_str._APS_Acyrthosiphon_pisum Buchnera_aphidicola_str._Bp_Baizongia_pistaciae Buchnera_aphidicola_str._Cc_Cinara_cedri Buchnera_aphidicola_str._Sg_Schizaphis_graminum Burkholderia_ambifaria_AMMD Burkholderia_ambifaria_MC40_6 Burkholderia_cenocepacia_AU_1054 Burkholderia_cenocepacia_HI2424 Burkholderia_cenocepacia_MC0_3 Burkholderia_mallei_ATCC_23344 Burkholderia_mallei_NCTC_10229 Burkholderia_mallei_NCTC_10247 Burkholderia_mallei_SAVP1 Burkholderia_multivorans_ATCC_17616 Burkholderia_phymatum_STM815 Burkholderia_phytofirmans_PsJN Burkholderia_pseudomallei_1106a Burkholderia_pseudomallei_1710b Burkholderia_pseudomallei_668 Burkholderia_pseudomallei_K96243 Burkholderia_sp._383 Burkholderia_thailandensis_E264 Burkholderia_vietnamiensis_G4 Burkholderia_xenovorans_LB400 Caldicellulosiruptor_saccharolyticus_DSM_8903 Campylobacter_concisus_13826 Campylobacter_curvus_525_92 'Campylobacter fetus subsp. fetus 82-40' Campylobacter_hominis_ATCC_BAA_381 Campylobacter_jejuni_RM1221 Campylobacter_jejuni_subsp._doylei_269_97 Campylobacter_jejuni_subsp._jejuni_81_176 Campylobacter_jejuni_subsp._jejuni_81116 Campylobacter_jejuni_subsp._jejuni_NCTC_11168 Candidatus_Amoebophilus_asiaticus_5a2 Candidatus_Blochmannia_floridanus Candidatus_Blochmannia_pennsylvanicus_str._BPEN Candidatus_Desulfococcus_oleovorans_Hxd3 Candidatus_Desulforudis_audaxviator_MP104C Candidatus_Pelagibacter_ubique_HTCC1062 Candidatus_Phytoplasma_mali Candidatus_Protochlamydia_amoebophila_UWE25 'Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica)' Candidatus_Sulcia_muelleri_GWSS Candidatus_Vesicomyosocius_okutanii_HA Capnocytophaga_ochracea Carboxydothermus_hydrogenoformans_Z_2901 Catenulispora_acidiphila Caulobacter_crescentus_CB15 Caulobacter_sp._K31 Cellulomonas_flavigena Cellvibrio_japonicus_Ueda107 Chitinophaga_pinensis Chlamydia_muridarum_Nigg Chlamydia_trachomatis_434_Bu Chlamydia_trachomatis_A_HAR_13 Chlamydia_trachomatis_D_UW_3_CX Chlamydia_trachomatis_L2b_UCH_1_proctitis Chlamydophila_abortus_S26_3 Chlamydophila_caviae_GPIC Chlamydophila_felis_Fe_C_56 Chlamydophila_pneumoniae_AR39 Chlamydophila_pneumoniae_CWL029 Chlamydophila_pneumoniae_J138 Chlamydophila_pneumoniae_TW_183 Chlorobaculum_parvum_NCIB_8327 Chlorobium_chlorochromatii_CaD3 Chlorobium_limicola_DSM_245 Chlorobium_phaeobacteroides_BS1 Chlorobium_phaeobacteroides_DSM_266 Chlorobium_tepidum_TLS Chloroflexus_aurantiacus_J_10_fl Chloroherpeton_thalassium_ATCC_35110 Chromobacterium_violaceum_ATCC_12472 Chromohalobacter_salexigens_DSM_3043 Citrobacter_koseri_ATCC_BAA_895 Clavibacter_michiganensis_subsp._michiganensis_NCPPB_382 Clavibacter_michiganensis_subsp._sepedonicus Clostridium_acetobutylicum_ATCC_824 Clostridium_beijerinckii_NCIMB_8052 Clostridium_botulinum_A_str._ATCC_19397 Clostridium_botulinum_A_str._ATCC_3502 Clostridium_botulinum_A_str._Hall Clostridium_botulinum_A3_str._Loch_Maree Clostridium_botulinum_B_str._Eklund_17B Clostridium_botulinum_B1_str._Okra Clostridium_botulinum_E3_str._Alaska_E43 Clostridium_botulinum_F_str._Langeland Clostridium_difficile_630 Clostridium_kluyveri_DSM_555 Clostridium_novyi_NT Clostridium_perfringens_ATCC_13124 Clostridium_perfringens_SM101 Clostridium_perfringens_str._13 Clostridium_phytofermentans_ISDg Clostridium_tetani_E88 Clostridium_thermocellum_ATCC_27405 Colwellia_psychrerythraea_34H Conexibacter_woesei Corynebacterium_diphtheriae_NCTC_13129 Corynebacterium_efficiens_YS_314 Corynebacterium_glutamicum_ATCC_13032 Corynebacterium_glutamicum_R Corynebacterium_jeikeium_K411 Corynebacterium_urealyticum_DSM_7109 Coxiella_burnetii_Dugway_5J108_111 Coxiella_burnetii_RSA_331 Coxiella_burnetii_RSA_493 Cryptobacterium_curtum Cupriavidus_taiwanensis Cyanothece_sp._ATCC_51142 Cytophaga_hutchinsonii_ATCC_33406 Dechloromonas_aromatica_RCB Dehalococcoides_ethenogenes_195 Dehalococcoides_sp._BAV1 Dehalococcoides_sp._CBDB1 Deinococcus_geothermalis_DSM_11300 Deinococcus_radiodurans_R1 Delftia_acidovorans_SPH_1 Denitrovibrio_acetiphilus Desulfitobacterium_hafniense_Y51 Desulfohalobium_retbaense Desulfomicrobium_baculatum Desulfotalea_psychrophila_LSv54 Desulfotomaculum_acetoxidans Desulfotomaculum_reducens_MI_1 Desulfovibrio_desulfuricans_subsp._desulfuricans_str._G20 Desulfovibrio_vulgaris_subsp._vulgaris_DP4 Desulfovibrio_vulgaris_subsp._vulgaris_str._Hildenborough Dethiosulfovibrio_peptidovorans Dichelobacter_nodosus_VCS1703A Dinoroseobacter_shibae_DFL_12 Dyadobacter_fermentans Eggerthella_lenta Ehrlichia_canis_str._Jake Ehrlichia_chaffeensis_str._Arkansas Ehrlichia_ruminantium_str._Gardel Ehrlichia_ruminantium_str._Welgevonden Elusimicrobium_minutum_Pei191 Enterobacter_sakazakii_ATCC_BAA_894 Enterobacter_sp._638 Enterococcus_faecalis_V583 Erwinia_carotovora_subsp._atroseptica_SCRI1043 Erwinia_tasmaniensis Erythrobacter_litoralis_HTCC2594 Escherichia_coli_536 Escherichia_coli_APEC_O1 Escherichia_coli_ATCC_8739 Escherichia_coli_CFT073 Escherichia_coli_E24377A Escherichia_coli_HS Escherichia_coli_O157_H7_EDL933 Escherichia_coli_O157_H7_str._Sakai Escherichia_coli_SMS_3_5 Escherichia_coli_UTI89 Escherichia_coli_str._K12_substr_DH10B Escherichia_coli_str._K12_substr_MG1655 Exiguobacterium_sibiricum_255_15 Fervidobacterium_nodosum_Rt17_B1 Finegoldia_magna_ATCC_29328 Flavobacterium_johnsoniae_UW101 Flavobacterium_psychrophilum_JIP02_86 Francisella_philomiragia_subsp._philomiragia_ATCC_25017 Francisella_tularensis_subsp._holarctica Francisella_tularensis_subsp._holarctica_FTNF002_00 Francisella_tularensis_subsp._holarctica_OSU18 Francisella_tularensis_subsp._mediasiatica_FSC147 Francisella_tularensis_subsp._novicida_U112 Francisella_tularensis_subsp._tularensis_FSC198 Francisella_tularensis_subsp._tularensis_SCHU_S4 Francisella_tularensis_subsp._tularensis_WY96_3418 Frankia_alni_ACN14a Frankia_sp._CcI3 Frankia_sp._EAN1pec Fusobacterium_nucleatum_subsp._nucleatum_ATCC_25586 Geobacillus_kaustophilus_HTA426 Geobacillus_thermodenitrificans_NG80_2 Geobacter_lovleyi_SZ Geobacter_metallireducens_GS_15 Geobacter_sulfurreducens_PCA Geobacter_uraniumreducens_Rf4 Geodermatophilus_obscurus Gloeobacter_violaceus_PCC_7421 Gluconacetobacter_diazotrophicus_PAl_5 Gluconobacter_oxydans_621H Gordonia_bronchialis Gramella_forsetii_KT0803 Granulibacter_bethesdensis_CGDNIH1 Haemophilus_ducreyi_35000HP Haemophilus_influenzae_86_028NP Haemophilus_influenzae_PittEE Haemophilus_influenzae_PittGG Haemophilus_influenzae_Rd_KW20 Haemophilus_somnus_129PT Haemophilus_somnus_2336 Hahella_chejuensis_KCTC_2396 Haliangium_ochraceum Halorhodospira_halophila_SL1 Helicobacter_acinonychis_str._Sheeba Helicobacter_hepaticus_ATCC_51449 Helicobacter_pylori_26695 Helicobacter_pylori_HPAG1 Helicobacter_pylori_J99 Helicobacter_pylori_Shi470 Heliobacterium_modesticaldum_Ice1 Herminiimonas_arsenicoxydans Herpetosiphon_aurantiacus_ATCC_23779 Hyphomonas_neptunium_ATCC_15444 Idiomarina_loihiensis_L2TR Jannaschia_sp._CCS1 Janthinobacterium_sp._Marseille Jonesia_denitrificans Kangiella_koreensis Kineococcus_radiotolerans_SRS30216 Klebsiella_pneumoniae_subsp._pneumoniae_MGH_78578 Kocuria_rhizophila_DC2201 Kribbella_flavida Kytococcus_sedentarius Lactobacillus_acidophilus_NCFM Lactobacillus_brevis_ATCC_367 Lactobacillus_casei_ATCC_334 Lactobacillus_casei_BL23 Lactobacillus_delbrueckii_subsp._bulgaricus_ATCC_11842 Lactobacillus_delbrueckii_subsp._bulgaricus_ATCC_BAA_365 Lactobacillus_fermentum_IFO_3956 Lactobacillus_gasseri_ATCC_33323 Lactobacillus_helveticus_DPC_4571 Lactobacillus_johnsonii_NCC_533 Lactobacillus_plantarum_WCFS1 Lactobacillus_reuteri_F275 Lactobacillus_sakei_subsp._sakei_23K Lactobacillus_salivarius_UCC118 Lactococcus_lactis_subsp._cremoris_MG1363 Lactococcus_lactis_subsp._cremoris_SK11 Lactococcus_lactis_subsp._lactis_Il1403 Lawsonia_intracellularis_PHE_MN1_00 Legionella_pneumophila_str._Corby Legionella_pneumophila_str._Lens Legionella_pneumophila_str._Paris Legionella_pneumophila_subsp._pneumophila_str._Philadelphia_1 Leifsonia_xyli_subsp._xyli_str._CTCB07 Leptospira_biflexa_serovar_Patoc_strain_Patoc_1_Ames Leptospira_biflexa_serovar_Patoc_strain_Patoc_1_Paris 'Leptospira borgpetersenii serovar Hardjo-bovis JB197' 'Leptospira borgpetersenii serovar Hardjo-bovis L550' Leptospira_interrogans_serovar_Copenhageni_str._Fiocruz_L1_130 Leptospira_interrogans_serovar_Lai_str._56601 Leptothrix_cholodnii_sp._6 Leptotrichia_buccalis Leuconostoc_citreum_KM20 Leuconostoc_mesenteroides_subsp._mesenteroides_ATCC_8293 Listeria_innocua_Clip11262 Listeria_monocytogenes_EGD_e Listeria_monocytogenes_str._4b_F2365 Listeria_welshimeri_serovar_6b_str._SLCC5334 Lysinibacillus_sphaericus_C3_41 'Magnetococcus sp. MC-1' Magnetospirillum_magneticum_AMB_1 Mannheimia_succiniciproducens_MBEL55E Maricaulis_maris_MCS10 Marinobacter_aquaeolei_VT8 Marinomonas_sp._MWYL1 Meiothermus_ruber Meiothermus_silvanus Mesoplasma_florum_L1 Mesorhizobium_loti_MAFF303099 Mesorhizobium_sp._BNC1 Methylacidiphilum_infernorum_V4 Methylibium_petroleiphilum_PM1 Methylobacillus_flagellatus_KT Methylobacterium_extorquens_PA1 Methylobacterium_populi_BJ001 Methylobacterium_radiotolerans_JCM_2831 Methylobacterium_sp._4_46 Methylococcus_capsulatus_str._Bath Microcystis_aeruginosa_NIES_843 Moorella_thermoacetica_ATCC_39073 Mycobacterium_abscessus Mycobacterium_avium_104 Mycobacterium_avium_subsp._paratuberculosis_K_10 Mycobacterium_bovis_AF2122_97 Mycobacterium_bovis_BCG_str._Pasteur_1173P2 Mycobacterium_gilvum_PYR_GCK Mycobacterium_leprae_TN Mycobacterium_marinum_M Mycobacterium_smegmatis_str._MC2_155 Mycobacterium_sp._JLS Mycobacterium_sp._KMS Mycobacterium_sp._MCS Mycobacterium_tuberculosis_CDC1551 Mycobacterium_tuberculosis_F11 Mycobacterium_tuberculosis_H37Ra Mycobacterium_tuberculosis_H37Rv Mycobacterium_ulcerans_Agy99 Mycobacterium_vanbaalenii_PYR_1 Mycoplasma_agalactiae_PG2 Mycoplasma_arthritidis_158L3_1 Mycoplasma_capricolum_subsp._capricolum_ATCC_27343 Mycoplasma_gallisepticum_R Mycoplasma_genitalium_G37 Mycoplasma_hyopneumoniae_232 Mycoplasma_hyopneumoniae_7448 Mycoplasma_hyopneumoniae_J Mycoplasma_mobile_163K Mycoplasma_mycoides_subsp._mycoides_SC_str._PG1 Mycoplasma_penetrans_HF_2 Mycoplasma_pneumoniae_M129 Mycoplasma_pulmonis_UAB_CTIP Mycoplasma_synoviae_53 Myxococcus_xanthus_DK_1622 Nakamurella_multipartita Natranaerobius_thermophilus_JW_NM_WN_LF Neisseria_gonorrhoeae_FA_1090 Neisseria_gonorrhoeae_NCCP11945 Neisseria_meningitidis_053442 Neisseria_meningitidis_FAM18 Neisseria_meningitidis_MC58 Neisseria_meningitidis_Z2491 Neorickettsia_sennetsu_str._Miyayama Nitratiruptor_sp._SB155_2 Nitrobacter_hamburgensis_X14 Nitrobacter_winogradskyi_Nb_255 Nitrosococcus_oceani_ATCC_19707 Nitrosomonas_europaea_ATCC_19718 Nitrosomonas_eutropha_C91 Nitrosospira_multiformis_ATCC_25196 Nocardia_farcinica_IFM_10152 Nocardioides_sp._JS614 Nocardiopsis_dassonvillei Nostoc_punctiforme_PCC_73102 Nostoc_sp._PCC_7120 Novosphingobium_aromaticivorans_DSM_12444 Oceanobacillus_iheyensis_HTE831 Ochrobactrum_anthropi_ATCC_49188 Oenococcus_oeni_PSU_1 'Onion yellows phytoplasma OY-M' Opitutus_terrae_PB90_1 Orientia_tsutsugamushi_Boryong Orientia_tsutsugamushi_str._Ikeda Parabacteroides_distasonis_ATCC_8503 Paracoccus_denitrificans_PD1222 Parvibaculum_lavamentivorans_DS_1 Pasteurella_multocida_subsp._multocida_str._Pm70 Pediococcus_pentosaceus_ATCC_25745 Pedobacter_heparinus Pelobacter_carbinolicus_DSM_2380 Pelobacter_propionicus_DSM_2379 Pelodictyon_luteolum_DSM_273 Pelotomaculum_thermopropionicum_SI Petrotoga_mobilis_SJ95 Photobacterium_profundum_SS9 Photorhabdus_luminescens_subsp._laumondii_TTO1 Planctomyces_limnophilus Polaromonas_naphthalenivorans_CJ2 Polaromonas_sp._JS666 Polynucleobacter_necessarius_STIR1 'Polynucleobacter sp. QLW-P1DMWA-1' Porphyromonas_gingivalis_ATCC_33277 Porphyromonas_gingivalis_W83 Prochlorococcus_marinus_str._AS9601 Prochlorococcus_marinus_str._MIT_9211 Prochlorococcus_marinus_str._MIT_9215 Prochlorococcus_marinus_str._MIT_9301 Prochlorococcus_marinus_str._MIT_9303 Prochlorococcus_marinus_str._MIT_9312 Prochlorococcus_marinus_str._MIT_9313 Prochlorococcus_marinus_str._MIT_9515 Prochlorococcus_marinus_str._NATL1A Prochlorococcus_marinus_str._NATL2A Prochlorococcus_marinus_subsp._marinus_str._CCMP1375 Prochlorococcus_marinus_subsp._pastoris_str._CCMP1986 Propionibacterium_acnes_KPA171202 Prosthecochloris_vibrioformis_DSM_265 Pseudoalteromonas_atlantica_T6c Pseudoalteromonas_haloplanktis_TAC125 Pseudomonas_aeruginosa_PA7 Pseudomonas_aeruginosa_PAO1 Pseudomonas_aeruginosa_UCBPP_PA14 Pseudomonas_entomophila_L48 Pseudomonas_fluorescens_Pf_5 Pseudomonas_fluorescens_PfO_1 Pseudomonas_mendocina_ymp Pseudomonas_putida_F1 Pseudomonas_putida_GB_1 Pseudomonas_putida_KT2440 Pseudomonas_putida_W619 Pseudomonas_stutzeri_A1501 Pseudomonas_syringae_pv._phaseolicola_1448A Pseudomonas_syringae_pv._syringae_B728a Pseudomonas_syringae_pv._tomato_str._DC3000 Psychrobacter_arcticus_273_4 Psychrobacter_cryohalolentis_K5 'Psychrobacter sp. PRwf-1' Psychromonas_ingrahamii_37 Ralstonia_eutropha_H16 Ralstonia_eutropha_JMP134 Ralstonia_metallidurans_CH34 Ralstonia_pickettii_12J Ralstonia_solanacearum_GMI1000 Renibacterium_salmoninarum_ATCC_33209 Rhizobium_etli_CFN_42 Rhizobium_etli_CIAT_652 Rhizobium_leguminosarum_bv._viciae_3841 Rhodobacter_sphaeroides_2_4_1 Rhodobacter_sphaeroides_ATCC_17025 Rhodobacter_sphaeroides_ATCC_17029 Rhodococcus_sp._RHA1 Rhodoferax_ferrireducens_T118 Rhodopirellula_baltica_SH_1 Rhodopseudomonas_palustris_BisA53 Rhodopseudomonas_palustris_BisB18 Rhodopseudomonas_palustris_BisB5 Rhodopseudomonas_palustris_CGA009 Rhodopseudomonas_palustris_HaA2 Rhodopseudomonas_palustris_TIE_1 Rhodospirillum_rubrum_ATCC_11170 Rhodothermus_marinus Rickettsia_akari_str._Hartford Rickettsia_bellii_OSU_85_389 Rickettsia_bellii_RML369_C Rickettsia_canadensis_str._McKiel Rickettsia_conorii_str._Malish_7 Rickettsia_felis_URRWXCal2 Rickettsia_massiliae_MTU5 Rickettsia_prowazekii_str._Madrid_E Rickettsia_rickettsii_str._Iowa Rickettsia_rickettsii_str._Sheila_Smith Rickettsia_typhi_str._Wilmington Roseiflexus_castenholzii_DSM_13941 'Roseiflexus sp. RS-1' Roseobacter_denitrificans_OCh_114 Rubrobacter_xylanophilus_DSM_9941 Saccharomonospora_viridis Saccharophagus_degradans_2_40 Saccharopolyspora_erythraea_NRRL_2338 Salinibacter_ruber_DSM_13855 Salinispora_arenicola_CNS_205 Salinispora_tropica_CNB_440 Salmonella_enterica_subsp._arizonae_serovar_62_z4_z23 Salmonella_enterica_subsp._enterica_serovar_Choleraesuis_str._SC_B67 Salmonella_enterica_subsp._enterica_serovar_Paratyphi_A_str._ATCC_9150 Salmonella_enterica_subsp._enterica_serovar_Paratyphi_B_str._SPB7 Salmonella_enterica_subsp._enterica_serovar_Typhi_str._CT18 Salmonella_enterica_subsp._enterica_serovar_Typhi_str._Ty2 Salmonella_typhimurium_LT2 Sanguibacter_keddieii Sebaldella_termitidis Serratia_proteamaculans_568 Shewanella_amazonensis_SB2B Shewanella_baltica_OS155 Shewanella_baltica_OS185 Shewanella_baltica_OS195 Shewanella_denitrificans_OS217 Shewanella_frigidimarina_NCIMB_400 Shewanella_halifaxensis_HAW_EB4 Shewanella_loihica_pv._4 Shewanella_oneidensis_MR_1 Shewanella_pealeana_ATCC_700345 Shewanella_putrefaciens_CN_32 Shewanella_sediminis_HAW_EB3 'Shewanella sp. ANA-3' 'Shewanella sp. MR-4' 'Shewanella sp. MR-7' Shewanella_sp._W3_18_1 Shewanella_woodyi_ATCC_51908 Shigella_boydii_CDC_3083_94 Shigella_boydii_Sb227 Shigella_dysenteriae_Sd197 Shigella_flexneri_2a_str._2457T Shigella_flexneri_2a_str._301 Shigella_flexneri_5_str._8401 Shigella_sonnei_Ss046 Silicibacter_pomeroyi_DSS_3 Silicibacter_sp._TM1040 Sinorhizobium_medicae_WSM419 Sinorhizobium_meliloti_1021 Slackia_heliotrinireducens Sodalis_glossinidius_str._morsitans Solibacter_usitatus_Ellin6076 Sorangium_cellulosum_So_ce_56 Sphaerobacter_thermophilus Sphingomonas_wittichii_RW1 Sphingopyxis_alaskensis_RB2256 Spirosoma_linguale Stackebrandtia_nassauensis Staphylococcus_aureus_RF122 Staphylococcus_aureus_subsp._aureus_COL Staphylococcus_aureus_subsp._aureus_JH1 Staphylococcus_aureus_subsp._aureus_JH9 Staphylococcus_aureus_subsp._aureus_MRSA252 Staphylococcus_aureus_subsp._aureus_MSSA476 Staphylococcus_aureus_subsp._aureus_MW2 Staphylococcus_aureus_subsp._aureus_Mu3 Staphylococcus_aureus_subsp._aureus_Mu50 Staphylococcus_aureus_subsp._aureus_N315 Staphylococcus_aureus_subsp._aureus_NCTC_8325 Staphylococcus_aureus_subsp._aureus_USA300 Staphylococcus_aureus_subsp._aureus_USA300_TCH1516 Staphylococcus_aureus_subsp._aureus_str._Newman Staphylococcus_epidermidis_ATCC_12228 Staphylococcus_epidermidis_RP62A Staphylococcus_haemolyticus_JCSC1435 Staphylococcus_saprophyticus_subsp._saprophyticus_ATCC_15305 Stenotrophomonas_maltophilia_K279a Streptobacillus_moniliformis Streptococcus_agalactiae_2603V_R Streptococcus_agalactiae_A909 Streptococcus_agalactiae_NEM316 Streptococcus_gordonii_str._Challis_substr_CH1 Streptococcus_mutans_UA159 Streptococcus_pneumoniae_CGSP14 Streptococcus_pneumoniae_D39 Streptococcus_pneumoniae_Hungary19A_6 Streptococcus_pneumoniae_R6 Streptococcus_pneumoniae_TIGR4 Streptococcus_pyogenes_M1_GAS Streptococcus_pyogenes_MGAS10270 Streptococcus_pyogenes_MGAS10394 Streptococcus_pyogenes_MGAS10750 Streptococcus_pyogenes_MGAS2096 Streptococcus_pyogenes_MGAS315 Streptococcus_pyogenes_MGAS5005 Streptococcus_pyogenes_MGAS6180 Streptococcus_pyogenes_MGAS8232 Streptococcus_pyogenes_MGAS9429 Streptococcus_pyogenes_SSI_1 Streptococcus_pyogenes_str._Manfredo Streptococcus_sanguinis_SK36 Streptococcus_suis_05ZYH33 Streptococcus_suis_98HAH33 Streptococcus_thermophilus_CNRZ1066 Streptococcus_thermophilus_LMD_9 Streptococcus_thermophilus_LMG_18311 Streptomyces_avermitilis_MA_4680 Streptomyces_coelicolor_A3_2 Streptomyces_griseus_subsp._griseus_NBRC_13350 Streptosporangium_roseum Sulfurihydrogenibium_sp._YO3AOP1 Sulfurimonas_denitrificans_DSM_1251 Sulfurospirillum_deleyianum Sulfurovum_sp._NBC37_1 Symbiobacterium_thermophilum_IAM_14863 Synechococcus_elongatus_PCC_6301 Synechococcus_elongatus_PCC_7942 Synechococcus_sp._CC9311 Synechococcus_sp._CC9605 Synechococcus_sp._CC9902 'Synechococcus sp. JA-2-3B''a(2-13)' 'Synechococcus sp. JA-3-3Ab' Synechococcus_sp._PCC_7002 Synechococcus_sp._RCC307 Synechococcus_sp._WH_7803 Synechococcus_sp._WH_8102 Synechocystis_sp._PCC_6803 Syntrophobacter_fumaroxidans_MPOB Syntrophomonas_wolfei_subsp._wolfei_str._Goettingen Syntrophus_aciditrophicus_SB Thermanaerovibrio_acidaminovorans Thermoanaerobacter_pseudethanolicus_ATCC_33223 Thermoanaerobacter_sp._X514 Thermoanaerobacter_tengcongensis_MB4 Thermobaculum_terrenum Thermobifida_fusca_YX Thermobispora_bispora Thermomonospora_curvata Thermosipho_melanesiensis_BI429 Thermosynechococcus_elongatus_BP_1 Thermotoga_lettingae_TMO Thermotoga_maritima_MSB8 Thermotoga_petrophila_RKU_1 Thermotoga_sp._RQ2 Thermus_thermophilus_HB27 Thermus_thermophilus_HB8 Thiobacillus_denitrificans_ATCC_25259 Thiomicrospira_crunogena_XCL_2 Treponema_denticola_ATCC_35405 Treponema_pallidum_subsp._pallidum_SS14 Treponema_pallidum_subsp._pallidum_str._Nichols Trichodesmium_erythraeum_IMS101 Tropheryma_whipplei_TW08_27 Tropheryma_whipplei_str._Twist Tsukamurella_paurometabola Ureaplasma_parvum_serovar_3_str._ATCC_27815 Ureaplasma_parvum_serovar_3_str._ATCC_700970 Veillonella_parvula Verminephrobacter_eiseniae_EF01_2 Vibrio_cholerae_O1_biovar_eltor_str._N16961 Vibrio_cholerae_O395 Vibrio_fischeri_ES114 Vibrio_harveyi_ATCC_BAA_1116 Vibrio_parahaemolyticus_RIMD_2210633 Vibrio_vulnificus_CMCP6 Vibrio_vulnificus_YJ016 Wigglesworthia_glossinidia_endosymbiont_of_Glossina_brevipalpis Wolbachia_endosymbiont_of_Drosophila_melanogaster Wolbachia_endosymbiont_strain_TRS_of_Brugia_malayi Wolbachia_pipientis Wolinella_succinogenes_DSM_1740 Xanthobacter_autotrophicus_Py2 Xanthomonas_axonopodis_pv._citri_str._306 Xanthomonas_campestris_pv._campestris Xanthomonas_campestris_pv._campestris_str._8004 Xanthomonas_campestris_pv._campestris_str._ATCC_33913 Xanthomonas_campestris_pv._vesicatoria_str._85_10 Xanthomonas_oryzae_pv._oryzae_KACC10331 Xanthomonas_oryzae_pv._oryzae_MAFF_311018 Xanthomonas_oryzae_pv._oryzae_PXO99A Xylanimonas_cellulosilytica Xylella_fastidiosa_9a5c Xylella_fastidiosa_M12 Xylella_fastidiosa_M23 Xylella_fastidiosa_Temecula1 Yersinia_enterocolitica_subsp._enterocolitica_8081 Yersinia_pestis_Angola Yersinia_pestis_Antiqua Yersinia_pestis_CO92 Yersinia_pestis_KIM Yersinia_pestis_Nepal516 Yersinia_pestis_Pestoides_F Yersinia_pestis_biovar_Microtus_str._91001 Yersinia_pseudotuberculosis_IP_31758 Yersinia_pseudotuberculosis_IP_32953 Yersinia_pseudotuberculosis_PB1 Yersinia_pseudotuberculosis_YPIII Zymomonas_mobilis_subsp._mobilis_ZM4 ; END; BEGIN TREES; TITLE GEBA_720_TB; LINK TAXA = Taxa; TREE phyml = [&R] (((((Thermanaerovibrio_acidaminovorans:0.190689,Dethiosulfovibrio_peptidovorans:0.263143):0.276658,((((((((((((((((((((((((((((((((((((((((Escherichia_coli_O157_H7_str._Sakai:0.0,Escherichia_coli_str._K12_substr_MG1655:0.0):1.51E-4,Escherichia_coli_str._K12_substr_DH10B:0.0):2.0E-5,(Escherichia_coli_ATCC_8739:1.7E-4,Escherichia_coli_HS:1.71E-4):1.7E-4):0.0,(Escherichia_coli_536:0.001196,Escherichia_coli_APEC_O1:0.0):0.0):0.0,((Shigella_flexneri_2a_str._301:0.001883,Shigella_flexneri_2a_str._2457T:0.0):1.71E-4,Shigella_flexneri_5_str._8401:3.44E-4):5.12E-4):0.0,(Shigella_boydii_CDC_3083_94:5.13E-4,Shigella_boydii_Sb227:8.57E-4):3.42E-4):0.0,Escherichia_coli_SMS_3_5:0.0):0.0,Escherichia_coli_O157_H7_EDL933:0.0):0.0,Escherichia_coli_CFT073:0.0):0.0,Escherichia_coli_UTI89:0.0):0.0,Escherichia_coli_E24377A:0.0):0.0,Shigella_dysenteriae_Sd197:0.001025):1.69E-4,Shigella_sonnei_Ss046:0.001028):0.012167,(((((((Salmonella_enterica_subsp._enterica_serovar_Typhi_str._Ty2:0.0,Salmonella_enterica_subsp._enterica_serovar_Typhi_str._CT18:1.7E-4):3.4E-4,Salmonella_typhimurium_LT2:0.0):0.0,Salmonella_enterica_subsp._enterica_serovar_Paratyphi_A_str._ATCC_9150:8.5E-4):2.0E-6,Salmonella_enterica_subsp._enterica_serovar_Paratyphi_B_str._SPB7:1.8E-4):1.69E-4,Salmonella_enterica_subsp._enterica_serovar_Choleraesuis_str._SC_B67:3.48E-4):0.001774,Salmonella_enterica_subsp._arizonae_serovar_62_z4_z23:0.001673):0.008533,Citrobacter_koseri_ATCC_BAA_895:0.007106):0.003103):0.00437,Klebsiella_pneumoniae_subsp._pneumoniae_MGH_78578:0.012094):0.004392,Enterobacter_sakazakii_ATCC_BAA_894:0.019781):0.007021,Enterobacter_sp._638:0.019532):0.027075,(Erwinia_tasmaniensis:0.033979,Serratia_proteamaculans_568:0.033607):0.013319):0.008604,Erwinia_carotovora_subsp._atroseptica_SCRI1043:0.03122):0.012206,((((((Yersinia_pestis_KIM:0.0,Yersinia_pseudotuberculosis_IP_31758:0.0):0.0,Yersinia_pestis_CO92:0.0):0.0,Yersinia_pseudotuberculosis_IP_32953:0.0):0.0,((((Yersinia_pseudotuberculosis_PB1:0.0,Yersinia_pestis_Pestoides_F:0.0):0.0,(Yersinia_pseudotuberculosis_YPIII:0.0,Yersinia_pestis_Nepal516:0.0):0.0):0.0,Yersinia_pestis_Antiqua:1.72E-4):0.0,Yersinia_pestis_biovar_Microtus_str._91001:0.0):0.0):0.0,Yersinia_pestis_Angola:3.44E-4):0.00575,Yersinia_enterocolitica_subsp._enterocolitica_8081:0.009468):0.030284):0.008222,((((Candidatus_Blochmannia_pennsylvanicus_str._BPEN:0.111832,Candidatus_Blochmannia_floridanus:0.199319):0.14508,(((Buchnera_aphidicola_str._APS_Acyrthosiphon_pisum:0.081646,Buchnera_aphidicola_str._Sg_Schizaphis_graminum:0.078489):0.090786,Buchnera_aphidicola_str._Bp_Baizongia_pistaciae:0.232468):0.043831,(Wigglesworthia_glossinidia_endosymbiont_of_Glossina_brevipalpis:0.30099,Buchnera_aphidicola_str._Cc_Cinara_cedri:0.303142):0.063766):0.064196):0.054991,Baumannia_cicadellinicola_str._Hc_Homalodisca_coagulata:0.166451):0.081445,Sodalis_glossinidius_str._morsitans:0.026696):0.024889):0.01239,Photorhabdus_luminescens_subsp._laumondii_TTO1:0.048195):0.050763,((((Haemophilus_somnus_129PT:9.73E-4,Haemophilus_somnus_2336:7.28E-4):0.038446,Pasteurella_multocida_subsp._multocida_str._Pm70:0.033371):0.011204,((Mannheimia_succiniciproducens_MBEL55E:0.02899,Actinobacillus_succinogenes_130Z:0.035825):0.013874,(((Haemophilus_influenzae_Rd_KW20:0.002043,Haemophilus_influenzae_PittGG:0.00105):5.49E-4,Haemophilus_influenzae_86_028NP:5.15E-4):2.24E-4,Haemophilus_influenzae_PittEE:0.001026):0.040304):0.008478):0.011217,(((Actinobacillus_pleuropneumoniae_L20:0.00137,Actinobacillus_pleuropneumoniae_serovar_7_str._AP76:3.39E-4):1.74E-4,Actinobacillus_pleuropneumoniae_serovar_3_str._JL03:0.003062):0.011765,Haemophilus_ducreyi_35000HP:0.024577):0.038512):0.080775):0.047571,(((((Vibrio_cholerae_O1_biovar_eltor_str._N16961:3.64E-4,Vibrio_cholerae_O395:8.38E-4):0.041305,(Vibrio_vulnificus_CMCP6:5.27E-4,Vibrio_vulnificus_YJ016:1.72E-4):0.020829):0.011445,(Vibrio_parahaemolyticus_RIMD_2210633:0.00625,Vibrio_harveyi_ATCC_BAA_1116:0.010839):0.011481):0.027253,Vibrio_fischeri_ES114:0.05376):0.027779,Photobacterium_profundum_SS9:0.072105):0.054993):0.023142,(Aeromonas_hydrophila_subsp._hydrophila_ATCC_7966:0.006284,Aeromonas_salmonicida_subsp._salmonicida_A449:0.0108):0.109795):0.020707,((((((Shewanella_halifaxensis_HAW_EB4:0.008905,Shewanella_pealeana_ATCC_700345:0.003805):0.025082,(Shewanella_sediminis_HAW_EB3:0.019306,Shewanella_woodyi_ATCC_51908:0.012326):0.017175):0.016987,Shewanella_loihica_pv._4:0.021173):0.024752,(((((('Shewanella sp. ANA-3':0.002092,'Shewanella sp. MR-4':9.8E-4):7.54E-4,'Shewanella sp. MR-7':3.48E-4):0.003036,Shewanella_oneidensis_MR_1:0.002265):0.010027,(Shewanella_sp._W3_18_1:3.26E-4,Shewanella_putrefaciens_CN_32:1.85E-4):0.001996):0.006463,((Shewanella_baltica_OS155:0.001236,Shewanella_baltica_OS195:0.0):5.23E-4,Shewanella_baltica_OS185:6.84E-4):0.009966):0.015626,(Shewanella_denitrificans_OS217:0.017657,Shewanella_frigidimarina_NCIMB_400:0.02512):0.022711):0.020469):0.018183,Shewanella_amazonensis_SB2B:0.035265):0.092511,Psychromonas_ingrahamii_37:0.170059):0.021406):0.025447,((Idiomarina_loihiensis_L2TR:0.129215,Pseudoalteromonas_atlantica_T6c:0.121204):0.026755,(Pseudoalteromonas_haloplanktis_TAC125:0.120366,Colwellia_psychrerythraea_34H:0.144993):0.031198):0.015669):0.082415,Kangiella_koreensis:0.172853):0.0486,((((((Acinetobacter_baumannii_ACICU:8.84E-4,Acinetobacter_baumannii_ATCC_17978:0.003413):5.27E-4,(Acinetobacter_baumannii_SDF:8.48E-4,Acinetobacter_baumannii_AYE:1.7E-4):0.0):0.020056,Acinetobacter_sp._ADP1:0.027905):0.107102,((Psychrobacter_arcticus_273_4:0.006888,Psychrobacter_cryohalolentis_K5:0.006086):0.066403,'Psychrobacter sp. PRwf-1':0.060503):0.121017):0.15381,Alcanivorax_borkumensis_SK2:0.175254):0.040455,(((Chromohalobacter_salexigens_DSM_3043:0.167612,Marinomonas_sp._MWYL1:0.175719):0.038094,(Marinobacter_aquaeolei_VT8:0.1125,Hahella_chejuensis_KCTC_2396:0.130701):0.053467):0.019075,(((((((((Pseudomonas_syringae_pv._syringae_B728a:0.001801,Pseudomonas_syringae_pv._phaseolicola_1448A:0.002321):0.002597,Pseudomonas_syringae_pv._tomato_str._DC3000:0.003918):0.02921,Pseudomonas_fluorescens_Pf_5:0.014609):0.00751,Pseudomonas_fluorescens_PfO_1:0.010753):0.026949,((((Pseudomonas_putida_KT2440:1.71E-4,Pseudomonas_putida_F1:0.0):0.001622,Pseudomonas_putida_GB_1:0.003034):0.003248,Pseudomonas_putida_W619:0.007868):0.003675,Pseudomonas_entomophila_L48:0.007306):0.02498):0.030505,Pseudomonas_mendocina_ymp:0.030084):0.018411,Pseudomonas_stutzeri_A1501:0.035067):0.021645,((Pseudomonas_aeruginosa_PAO1:0.0,Pseudomonas_aeruginosa_UCBPP_PA14:1.71E-4):0.001113,Pseudomonas_aeruginosa_PA7:0.001132):0.032184):0.118537,(Saccharophagus_degradans_2_40:0.107494,Cellvibrio_japonicus_Ueda107:0.109149):0.090952):0.024456):0.029903):0.041423):0.029921,(((Legionella_pneumophila_str._Corby:0.001506,Legionella_pneumophila_subsp._pneumophila_str._Philadelphia_1:5.43E-4):3.1E-4,(Legionella_pneumophila_str._Lens:0.00222,Legionella_pneumophila_str._Paris:0.001831):3.76E-4):0.255271,((Coxiella_burnetii_RSA_331:0.00102,Coxiella_burnetii_RSA_493:5.1E-4):0.001141,Coxiella_burnetii_Dugway_5J108_111:0.001413):0.286937):0.063734):0.020357,((((((((Francisella_tularensis_subsp._tularensis_SCHU_S4:0.0,Francisella_tularensis_subsp._tularensis_FSC198:0.0):0.001507,Francisella_tularensis_subsp._tularensis_WY96_3418:3.35E-4):3.34E-4,((Francisella_tularensis_subsp._holarctica_OSU18:0.0,Francisella_tularensis_subsp._holarctica:5.02E-4):0.0,Francisella_tularensis_subsp._holarctica_FTNF002_00:3.35E-4):0.002852):0.0,Francisella_tularensis_subsp._mediasiatica_FSC147:0.002516):0.001333,Francisella_tularensis_subsp._novicida_U112:6.81E-4):0.02679,Francisella_philomiragia_subsp._philomiragia_ATCC_25017:0.028537):0.343835,Dichelobacter_nodosus_VCS1703A:0.35117):0.058577,(('Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica)':0.048117,Candidatus_Vesicomyosocius_okutanii_HA:0.070088):0.299069,Thiomicrospira_crunogena_XCL_2:0.218606):0.069384):0.027865):0.019953,(((Halorhodospira_halophila_SL1:0.175731,Alkalilimnicola_ehrlichei_MLHE_1:0.10505):0.103584,Nitrosococcus_oceani_ATCC_19707:0.225193):0.031953,((((((Xanthomonas_campestris_pv._campestris_str._8004:3.43E-4,Xanthomonas_campestris_pv._campestris_str._ATCC_33913:5.15E-4):3.45E-4,Xanthomonas_campestris_pv._campestris:1.7E-4):0.006192,(((Xanthomonas_oryzae_pv._oryzae_KACC10331:1.75E-4,Xanthomonas_oryzae_pv._oryzae_MAFF_311018:0.0):0.0,Xanthomonas_oryzae_pv._oryzae_PXO99A:0.002957):0.008947,(Xanthomonas_campestris_pv._vesicatoria_str._85_10:0.001996,Xanthomonas_axonopodis_pv._citri_str._306:0.00127):0.004934):0.005782):0.031343,Stenotrophomonas_maltophilia_K279a:0.060056):0.030521,(((Xylella_fastidiosa_M23:0.0,Xylella_fastidiosa_Temecula1:1.74E-4):0.005446,Xylella_fastidiosa_M12:0.003419):0.005622,Xylella_fastidiosa_9a5c:0.003688):0.09616):0.251782,Methylococcus_capsulatus_str._Bath:0.208011):0.028921):0.02517):0.056558,((((((Nitrosomonas_europaea_ATCC_19718:0.04084,Nitrosomonas_eutropha_C91:0.04959):0.144982,Nitrosospira_multiformis_ATCC_25196:0.08516):0.076439,Thiobacillus_denitrificans_ATCC_25259:0.145726):0.023371,Methylobacillus_flagellatus_KT:0.155554):0.027233,(((Azoarcus_sp._BH72:0.052172,Azoarcus_sp._EbN1:0.058776):0.062917,Dechloromonas_aromatica_RCB:0.113139):0.05407,(((((('Polynucleobacter sp. 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TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr25470] END;