#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 April 24, 2024; 2:55 GMT TreeBASE (cc) 1994-2008 Study reference: Corthals A., Koller A., Martin D., Rieger R., Chen E., Bernaski M., Recagno G., & Davalos L.M. 2012. Detecting the Immune System Response of a 500 Year-old Inca Mummy. PLoS One, 7(7): e41244. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S11376] BEGIN TAXA; TITLE GenBank_refseq_matching_uncultured_bacterials_seqs; DIMENSIONS NTAX=74; TAXLABELS Acidothermus_cellulolyticus_11B Amycolatopsis_mediterranei_U32_chromosome Arthrobacter_chlorophenolicus_A6 Arthrobacter_sp__FB24_1 Bifidobacterium_adolescentis_ATCC_15703 Bifidobacterium_bifidum_PRL2010 Bifidobacterium_bifidum_S17 Bifidobacterium_breve_DSM_20213_B_breve1_0_1 Bifidobacterium_dentium_ATCC_27679 Bifidobacterium_dentium_Bd1 Bifidobacterium_longum_DJO10A Bifidobacterium_longum_NCC2705 Bifidobacterium_longum_infantis_157F Bifidobacterium_longum_infantis_ATCC_15697 Bifidobacterium_longum_infantis_ATCC_55813_ Bifidobacterium_longum_longum_BBMN68 Bifidobacterium_longum_longum_JCM_1217 Bifidobacterium_longum_longum_JDM301_chromo Bifidobacterium_sp._41_42 Catenulispora_acidiphila_DSM_44928 Cellulomonas_flavigena_DSM_20109 Clavibacter_michiganensis_michiganensis_NCP Clavibacter_michiganensis_sepedonicus Corynebacterium_efficiens_YS314 Corynebacterium_genitalium_ATCC_33030 Corynebacterium_glucuronolyticum_ATCC_51866 Corynebacterium_matruchotii_ATCC_14266 Corynebacterium_urealyticum_DSM_7109 Frankia_alni_ACN14a Geodermatophilus_obscurus_DSM_43160 Gordonia_bronchialis_DSM_43247 Intrasporangium_calvum_DSM_43043 Kineococcus_radiotolerans_SRS30216 Kocuria_rhizophila_DC2201 Kytococcus_sedentarius_DSM_20547_chromosome Micrococcus_luteus_NCTC_2665 Micromonospora_aurantiaca_ATCC_27029 Micromonospora_sp__L5 Mycobacterium_avium_104 Mycobacterium_avium_subsp__paratuberculosis_K10 Mycobacterium_bovis_AF2122_97 Mycobacterium_bovis_BCG_str__Pasteur_1173P2 Mycobacterium_bovis_BCG_str__Tokyo_172 Mycobacterium_gilvum_PYRGCK Mycobacterium_smegmatis_str__MC2_155 Mycobacterium_sp__JLS Mycobacterium_sp__KMS Mycobacterium_sp__MCS Mycobacterium_sp__Spyr1 Mycobacterium_sp._45_46 Mycobacterium_tuberculosis_CDC1551 Mycobacterium_tuberculosis_F11 Mycobacterium_tuberculosis_H37Ra Mycobacterium_tuberculosis_H37Rv Mycobacterium_tuberculosis_KZN_1435 Mycobacterium_vanbaalenii_PYR1 Nakamurella_multipartita_DSM_44233 Nocardia_farcinica_IFM_10152 Nocardioides_sp__JS614 Rhodococcus_equi_103S Rhodococcus_equi_ATCC_33707 Rhodococcus_jostii_RHA1 Rhodococcus_opacus_B4 Saccharopolyspora_erythraea_NRRL_2338 Salinispora_arenicola_CNS205 Salinispora_tropica_CNB440 Segniliparus_rotundus_DSM_44985 Streptomyces_avermitilis_MA4680 Streptomyces_coelicolor_A3_2_ Streptomyces_scabiei_87_22 Streptosporangium_roseum_DSM_43021 Thermobifida_fusca_YX Thermobispora_bispora_DSM_43833 Thermomonospora_curvata_DSM_43183 ; END; BEGIN TREES; TITLE Actinobacteria_reference_genomes_HSP65; LINK TAXA = GenBank_refseq_matching_uncultured_bacterials_seqs; TREE Best_tree = [&R] ((Mycobacterium_gilvum_PYRGCK:0.6136837377582963,(((Acidothermus_cellulolyticus_11B:0.19427499775760823,((Micromonospora_aurantiaca_ATCC_27029:0.0013284069612331437,Micromonospora_sp__L5:1.70179769852561E-6)100:0.034038978732829676,(Salinispora_tropica_CNB440:0.021570897791562328,Salinispora_arenicola_CNS205:0.012325458453079021)100:0.01953681006345278)100:0.06360704842814881)77:0.016208648407095943,((Streptosporangium_roseum_DSM_43021:0.11046171922362648,((Thermobifida_fusca_YX:0.17480314679047929,Thermobispora_bispora_DSM_43833:0.05315619070378082)46:0.024349009685905865,Thermomonospora_curvata_DSM_43183:0.10694847346709237)38:0.01150223882336332)78:0.03440093720159147,((Catenulispora_acidiphila_DSM_44928:0.13056173023515338,(Streptomyces_coelicolor_A3_2_:0.025551874916299382,(Streptomyces_avermitilis_MA4680:0.025748347108577554,Streptomyces_scabiei_87_22:0.031789682201472776)66:0.011415742200303898)100:0.05749540571373292)51:0.020782571334828304,((((Geodermatophilus_obscurus_DSM_43160:0.07997336292315532,(Nakamurella_multipartita_DSM_44233:0.10799665589657557,Saccharopolyspora_erythraea_NRRL_2338:0.09006389419724886)56:0.026257480645827034)18:0.006344766508610207,Amycolatopsis_mediterranei_U32_chromosome:0.29377659408186724)14:0.007813502444166719,((((Arthrobacter_sp__FB24_1:0.05952032778085017,Arthrobacter_chlorophenolicus_A6:0.04642689248971741)100:0.08914384184292877,(Kocuria_rhizophila_DC2201:0.1245523346913592,Micrococcus_luteus_NCTC_2665:0.07053023212491004)99:0.04113720613088165)92:0.023376978311268552,((Segniliparus_rotundus_DSM_44985:0.12400236035058188,(((Gordonia_bronchialis_DSM_43247:0.1008321953933124,Rhodococcus_opacus_B4:0.05747619789076037)84:0.018159082118805465,(Rhodococcus_equi_ATCC_33707:0.003885283663327737,Rhodococcus_equi_103S:5.329555578248112E-5)100:0.05779878059086)74:0.01571054808232159,(Nocardia_farcinica_IFM_10152:0.05843156584002286,(Mycobacterium_sp._45_46:0.11627102381022483,(((Mycobacterium_avium_subsp__paratuberculosis_K10:0.004101231003025292,Mycobacterium_avium_104:0.003323705761260801)100:0.027407214405499505,((((((Mycobacterium_bovis_BCG_str__Pasteur_1173P2:1.70179769852561E-6,Mycobacterium_tuberculosis_H37Ra:1.70179769852561E-6)3:1.70179769852561E-6,Mycobacterium_bovis_BCG_str__Tokyo_172:1.70179769852561E-6)1:1.70179769852561E-6,Mycobacterium_bovis_AF2122_97:1.70179769852561E-6)1:1.70179769852561E-6,Mycobacterium_tuberculosis_CDC1551:1.70179769852561E-6)1:1.70179769852561E-6,(Mycobacterium_tuberculosis_F11:1.70179769852561E-6,Mycobacterium_tuberculosis_KZN_1435:1.70179769852561E-6)11:1.70179769852561E-6)1:1.70179769852561E-6,Mycobacterium_tuberculosis_H37Rv:1.70179769852561E-6)100:0.10277997251213214)84:0.029878594054454314,(((Mycobacterium_vanbaalenii_PYR1:0.040333324581427216,Mycobacterium_sp__Spyr1:0.031232404208718437)96:0.0204945391037184,Mycobacterium_smegmatis_str__MC2_155:0.04238358355045818)42:0.009458201332939167,(Mycobacterium_sp__JLS:1.70179769852561E-6,(Mycobacterium_sp__KMS:1.70179769852561E-6,Mycobacterium_sp__MCS:1.70179769852561E-6)71:6.573422837430518E-4)100:0.045503708473727235)63:0.01856895293804404)63:0.020292557282644542)65:0.018601371665659484)55:0.016272694114076544)51:0.009724635790618887)70:0.02967218201129624,((Bifidobacterium_sp._41_42:2.3556655473980643E-4,((Bifidobacterium_breve_DSM_20213_B_breve1_0_1:0.027450834009215618,((Bifidobacterium_longum_infantis_ATCC_55813_:0.0020788536101681828,(Bifidobacterium_longum_longum_BBMN68:8.015661192375776E-4,(((Bifidobacterium_longum_NCC2705:1.70179769852561E-6,Bifidobacterium_longum_DJO10A:1.70179769852561E-6)21:1.70179769852561E-6,Bifidobacterium_longum_infantis_157F:1.70179769852561E-6)13:1.70179769852561E-6,Bifidobacterium_longum_longum_JCM_1217:1.70179769852561E-6)88:4.883957401600249E-4)71:0.0013116678308241303)98:0.00447847502871826,(Bifidobacterium_longum_longum_JDM301_chromo:0.0033397661987383336,Bifidobacterium_longum_infantis_ATCC_15697:0.003816770740272865)92:0.002700495717084699)99:0.019131660294373985)74:0.00839406948833312,((Bifidobacterium_bifidum_PRL2010:1.70179769852561E-6,Bifidobacterium_bifidum_S17:0.0013028756639373122)100:0.06641682954366766,(Bifidobacterium_adolescentis_ATCC_15703:0.04396792866441896,(Bifidobacterium_dentium_Bd1:0.004505316502477852,Bifidobacterium_dentium_ATCC_27679:0.0014606034132264142)100:0.04898477042078803)100:0.05975539987993842)75:0.04508919325087516)99:0.17138338249617843)100:0.15388525725401675,(Corynebacterium_urealyticum_DSM_7109:0.15802737364587702,((Corynebacterium_matruchotii_ATCC_14266:0.1799452532820841,Corynebacterium_efficiens_YS314:0.08606292106549619)78:0.027117811214661704,(Corynebacterium_genitalium_ATCC_33030:0.1543394203885156,Corynebacterium_glucuronolyticum_ATCC_51866:0.1392693482837836)43:0.02227319147717056)78:0.025684844512327172)100:0.05508330680685389)49:0.047479894093943126)20:0.015644436058097354)32:0.022637089021155188,(((Clavibacter_michiganensis_michiganensis_NCP:0.0023741955424999473,Clavibacter_michiganensis_sepedonicus:0.016650654535414654)100:0.11395380970659362,Cellulomonas_flavigena_DSM_20109:0.10379303243415251)92:0.03535354020841988,Kineococcus_radiotolerans_SRS30216:0.07023738367697611)50:0.01204937070995442)26:0.013564526293369258)6:0.012848555052953767,(Nocardioides_sp__JS614:0.10940191821215763,(Intrasporangium_calvum_DSM_43043:0.13340229076081964,Kytococcus_sedentarius_DSM_20547_chromosome:0.10058534903239628)37:0.017684057242254594)32:0.013148316305988212)11:0.027757321201899058)5:0.011485773722273693)15:0.012586441835640704)99:0.15160404636512945,Rhodococcus_jostii_RHA1:0.5552757114246312)84:0.14152743766355488):0.1647045160414936,Frankia_alni_ACN14a:0.1647045160414936); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr52818] END;