#NEXUS
begin trees;
	tree FlhA = [&R] (WP_0033490721_Bacillus_methanolicus:0.23666,WP_0713909231_Anaerobacillus_alkalidiazotrophicus:0.216237,(((((((((((((((MZQ815731_Paenibacillus_silvestris:2.0E-6,WP_2025561641_Paenibacillus_silvestris:2.0E-6)[&label="78.7/100"]:0.001727,((WP_1274510491_Paenibacillus_chondroitinus:0.001659,WP_1573212261_MULTISPECIES_Paenibacillus:0.001409)[&label="85.4/100"]:0.003088,(WP_1670562081_Paenibacillus_aceris:2.0E-6,WP_1935808761_Paenibacillus_aceris:2.0E-6)[&label="93.1/100"]:0.004743)[&label="86.3/86"]:0.002983)[&label="69.1/68"]:0.001494,NOV031521_Paenibacillus_planticolens:0.006089)[&label="97.1/100"]:0.012869,((WP_0686625641_Paenibacillus_oryzisoli:0.008076,WP_1731083791_Paenibacillus_qinlingensis:0.007963)[&label="99.3/100"]:0.024104,WP_1261449931_Paenibacillus_whitsoniae:0.033961)[&label="75.8/87"]:0.007087)[&label="83.3/84"]:0.005523,((WP_0794089451_Paenibacillus_ferrarius:0.00307,WP_1732169621_Paenibacillus_alba:0.003045)[&label="96.9/100"]:0.011885,WP_1890129161_Paenibacillus_marchantiophytorum:0.005847)[&label="95/100"]:0.014952)[&label="89/97"]:0.007828,(WP_0568328841_Paenibacillus_sp_Soil787:0.010723,WP_0573015451_MULTISPECIES_unclassified_Paenibacillus:0.004801)[&label="66.6/92"]:0.005463)[&label="74/92"]:0.008385,WP_1639425221_Paenibacillus_sp_SYPB3998:0.024517)[&label="68.3/99"]:0.01654,WP_1881741511_Paenibacillus_sp_WST5:0.01581)[&label="99.8/100"]:0.043254,WP_1347484451_Paenibacillus_athensensis:0.047713)[&label="97.5/100"]:0.038383,WP_0234847121_Paenibacillus_larvae:0.136568)[&label="93.4/97"]:0.032896,WP_0762327831_Paenibacillus_sp_FSL_H70331:0.101371)[&label="96.4/97"]:0.038121,WP_1130191221_Paenibacillus_sp_YN15:0.167414)[&label="97.7/97"]:0.034359,((OUM969651_Thermobacillus_sp_ZCTH02B1:0.128766,WP_0940434011_MULTISPECIES_unclassified_Cohnella:0.174437)[&label="15.2/18"]:0.036231,(WP_0285614181_Paenibacillus_pinihumi:0.099787,(SDT461151_Paenibacillaceae_bacterium_GAS479:2.0E-6,WP_0895230851_Paenibacillus_herberti:0.004647)[&label="100/100"]:0.173204)[&label="78.8/20"]:0.027341)[&label="96.3/92"]:0.041338)[&label="54.9/88"]:0.026637,(WP_0874328551_Paenibacillus_apiarius:2.0E-6,WP_2060965421_Paenibacillus_apiarius:0.001568)[&label="100/100"]:0.15648)[&label="100/100"]:0.183496,(((((((((((AGB406461_Halobacteroides_halobius_DSM_5150:2.0E-6,WP_1568012541_Halobacteroides_halobius:2.0E-6)[&label="100/100"]:0.146225,WP_2047000761_Halanaerobacter_jeridensis:0.170153)[&label="97.3/100"]:0.055696,(((TDX519141_Orenia_marismortui:2.0E-6,WP_2083243821_Orenia_marismortui:2.0E-6)[&label="100/100"]:0.070294,WP_0687166511_Orenia_metallireducens:0.113478)[&label="69.4/98"]:0.043909,WP_0273387081_Halonatronum_saccharophilum:0.142072)[&label="96.1/100"]:0.054234)[&label="99.9/100"]:0.115013,((SJZ645331_Selenihalanaerobacter_shriftii:0.105596,(WP_0132785751_Acetohalobium_arabaticum:0.041392,WP_2049890981_Sporohalobacter_salinus:0.015658)[&label="100/100"]:0.075237)[&label="44.9/91"]:0.017721,WP_0897471731_MULTISPECIES_unclassified_Candidatus_Frackibacter:0.07173)[&label="99.8/100"]:0.075463)[&label="97.2/100"]:0.073586,(WP_1270172121_Anoxybacter_fermentans:0.205741,(QTL998991_Halanaerobiaceae_bacterium_NS1:0.21708,SDD119881_Halanaerobium_congolense:0.195684)[&label="99.9/100"]:0.202656)[&label="97.8/100"]:0.089433)[&label="100/100",!name="Firmicutes_F"]:0.210235,(((((HFV107491_Firmicutes_bacterium:0.590587,((((((((((HDW949061_Chloroflexi_bacterium:0.002026,(HEE597511_Chloroflexi_bacterium:2.0E-6,HEW892741_Chloroflexi_bacterium:2.0E-6)[&label="0/60"]:2.0E-6)[&label="100/100"]:0.261454,HFX653011_Chloroflexi_bacterium:0.265832)[&label="21.6/31"]:0.023437,(MBI29397721_Chloroflexi_bacterium:0.243272,((MBM44170631_Chloroflexi_bacterium:0.164907,TAK253371_Chloroflexi_bacterium:0.110774)[&label="100/100"]:0.199105,HHS213321_Chloroflexi_bacterium:0.526387)[&label="67.5/47"]:0.055835)[&label="27.9/33"]:0.015752)[&label="97.7/97"]:0.076199,(MBI23229691_Chloroflexi_bacterium:0.00317,MBI45077911_Chloroflexi_bacterium:0.001945)[&label="100/100"]:0.395724)[&label="93.5/100"]:0.06243,((MBV91206681_Chloroflexi_bacterium:0.336981,MBI42143331_Chloroflexi_bacterium:0.614525)[&label="84.6/93"]:0.057459,(((GCA_0028982151:0.026268,((GCA_0110482751:0.0,GCA_0110577751:0.0):2.0E-6,GCA_0110547351:2.0E-6)[&label="97.1/100"]:0.024359)[&label="99.9/100"]:0.186511,(((KAA02377681_bacterium:0.025902,MBE75201601_Thermoflexaceae_bacterium:0.018498)[&label="100/100"]:0.09737,(((MBI27644321_Chloroflexi_bacterium:0.087083,MBK66621621_Thermoflexaceae_bacterium:0.091187)[&label="99.9/100"]:0.065894,MBA41810071_Anaerolinea_sp:0.108547)[&label="93.9/100"]:0.032402,(((MBK63198561_Dehalococcoidia_bacterium:2.0E-6,(MBK65603141_Dehalococcoidia_bacterium:2.0E-6,(MBK77261101_Dehalococcoidia_bacterium:0.00147,MBK73284311_Dehalococcoidia_bacterium:0.001473)[&label="0/33"]:2.0E-6)[&label="75.8/100"]:0.001469)[&label="100/100"]:0.090236,(NJD652881_Chloroflexi_bacterium:0.004652,PWB419291_Dehalococcoidia_bacterium:2.0E-6)[&label="100/100"]:0.092442)[&label="47.3/99"]: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	tree FliC = [&R] 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rophicus:0.000002)88.8/93:0.017350,WP_1029408641_MULTISPECIES_Vibrio:0.022784)100/100:0.102780)76.6/92:0.032231,WP_1674219981_Vibrio_hepatarius:0.077218)1.5/21:0.014344)99.8/100:0.110841)94.8/100:0.091015,(((((((((((((((((((HAS262471_Vibrio_sp:0.002976,(WP_0170932621_Vibrio_splendidus:0.000002,(WP_0610223271_Vibrio_splendidus:0.000002,WP_1081761191_Vibrio_splendidus:0.002982)84.5/100:0.002975)0/36:0.000002)95.7/99:0.011917,WP_1081184021_Vibrio_splendidus:0.002955)77.2/86:0.002965,(WP_0170841211_Vibrio_splendidus:0.000002,WP_0545416731_Vibrio_splendidus:0.002957)80.6/100:0.002964)78.6/77:0.002964,(WP_1024499501_Vibrio_splendidus:0.002961,WP_1023201541_Vibrio_sp_10N26151A7:0.002967)0/36:0.000002)0/29:0.000002,(WP_0170862661_Vibrio_splendidus:0.000002,WP_1827971151_Vibrio_sp_SG417:0.002965)0/40:0.000002)94.1/50:0.002962,WP_1081946311_Vibrio_splendidus:0.000002)0/26:0.000002,WP_1081960941_Vibrio_splendidus:0.002962)80.4/62:0.002977,(((WP_0655850411_MULTISPECIES_Vibrio:0.000002,WP_1024636461_Vibrio_splendidus:0.005959)0/32:0.000002,WP_0766459791_MULTISPECIES_Vibrio:0.002973)0/16:0.000002,(WP_1081224941_Vibrio_splendidus:0.000002,WP_1938359981_Vibrio_sp_OPT20:0.002967)85.5/100:0.002969)78.3/93:0.002976)80.5/95:0.002971,(WP_1023117321_Vibrio_lentus:0.000002,WP_1024350421_Vibrio_lentus:0.002970)84.4/98:0.002968)0/27:0.000002,WP_1042112361_Vibrio_lentus:0.002970)0/10:0.000002,(((((((WP_0545476261_Vibrio_splendidus:0.002972,WP_1146338781_Vibrio_splendidus:0.000002)78.5/98:0.002981,((WP_1022659741_Vibrio_lentus:0.000002,WP_1023492831_Vibrio_lentus:0.002985)0/47:0.000002,WP_1022866991_Vibrio_lentus:0.002983)88.4/97:0.005979)29.4/33:0.002965,(WP_0171036431_Vibrio_tasmaniensis:0.000002,WP_1353841041_Vibrio_tasmaniensis:0.005955)99.7/99:0.021019)0/10:0.000002,WP_1024853481_Vibrio_lentus:0.002973)0/8:0.000002,(((WP_0766683431_Vibrio_lentus:0.000002,WP_1025177221_Vibrio_lentus:0.002976)86.6/46:0.002975,WP_1928522191_Vibrio_lentus:0.002976)0/14:0.000002,((WP_0651109351_Vibrio_tasmaniensis:0.005939,WP_1025164611_Vibrio_splendidus:0.011964)0/24:0.000002,WP_1329699041_Vibrio_crassostreae:0.008968)0/9:0.000002)92/18:0.002977)0/7:0.000002,WP_0651031191_MULTISPECIES_Vibrio:0.000002)0/5:0.000002,(WP_1081926901_Vibrio_splendidus:0.005964,(WP_1713080561_Vibrio_splendidus:0.000002,WP_1713169771_Vibrio_splendidus:0.005952)88.1/62:0.005956)77.1/10:0.002973)0/8:0.000002)94.6/12:0.008983,(WP_0198216461_Vibrio_splendidus:0.002981,(WP_1455751681_Vibrio_crassostreae:0.002969,WP_0486612521_Vibrio_crassostreae:0.002978)0/25:0.000002)76.3/97:0.002975)87.5/14:0.005949,((WP_0486161261_Vibrio_coralliirubri:0.002978,WP_0506496071_Vibrio_sp_J231:0.002976)0/11:0.000002,(((WP_0506449731_Vibrio_sp_J212:0.002982,(WP_0610387421_Vibrio_coralliirubri:0.000002,WP_0528789251_Vibrio_coralliirubri:0.002985)86.9/92:0.002981)0/41:0.000002,WP_0506524011_Vibrio_sp_J217:0.002978)85.6/97:0.002986,WP_0506479061_Vibrio_sp_J24:0.014957)0/30:0.000002)78.3/94:0.002988)77.5/14:0.003001,(WP_0867151111_Vibrio_gigantis:0.008909,WP_2154044211_Vibrio_gigantis:0.008973)76.8/99:0.002979)95.1/14:0.019715,WP_1713694531_Vibrio_chagasii:0.011229)99.8/100:0.072576,WP_1524691321_Vibrio_sp_THAF190c:0.042487)100/100:0.109384,(((RBW640901_Vibrionales_bacterium_C3R12:0.011945,WP_1717560131_Vibrio_sp_03591:0.000002)88.7/100:0.005977,WP_1369954601_Vibrio_genomosp_F6:0.002987)78.4/100:0.003195,WP_0170542241_Vibrio_genomosp_F6:0.002793)99.9/100:0.088575)97.9/100:0.054467,(((((((WP_0424840421_Vibrio_diazotrophicus:0.002993,WP_1029666531_Vibrio_diazotrophicus:0.000002)0/54:0.000002,WP_1029527091_Vibrio_diazotrophicus:0.006007)94/94:0.006001,(WP_1029408651_Vibrio_diazotrophicus:0.000002,WP_1711378501_Vibrio_plantisponsor:0.002997)0/33:0.000002)0/17:0.000002,WP_1124048331_Vibrio_diazotrophicus:0.002996)0/71:0.000565,WP_1029630941_Vibrio_diazotrophicus:0.011470)100/100:0.178037,WP_0534095031_Vibrio_hepatarius:0.064982)23.2/92:0.042010,WP_1265747631_Vibrio_aquaticus:0.067308)97.9/100:0.060695)98.1/100:0.072209,(((WP_0044083941_Vibrio_nigripulchritudo:0.000002,WP_0459616391_Vibrio_nigripulchritudo:0.003015)82.1/100:0.003017,WP_0226139311_Vibrio_nigripulchritudo:0.000002)98.8/100:0.045589,((WP_1011128711_MULTISPECIES_Vibrio:0.005584,WP_1044020531_Vibrio_penaeicida:0.006476)94.4/100:0.015225,WP_1903337691_Vibrio_sp_S9_S30:0.006442)95.3/100:0.033068)100/100:0.127322)99.8/100:0.103213)78.7/97:0.058956,GCA_0027224551:0.395720)100/100:0.489909)93.2/100:0.110683)95.8/100:0.127597)100/100:0.346542)100/100:0.276818)97.6/100:0.025831);
	tree FliI = [&R] 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_3112_Geobacillus_sp_B4113_201601:0.000002,WP_0827993311_Geobacillus_sp_B4113_201601:0.000002)92.8/100:0.005517)0/24:0.000002,WP_0818971951_MULTISPECIES_Geobacillus:0.000002)91.3/66:0.002769,WP_1449737321_Geobacillus_sp_C56T2:0.000002)0/24:0.000002,TWG300761_type_III_secretion_system_Geobacillus_sp_C56T2:0.000002)100/100:0.056025,((((((((((((((((ADI273011_Geobacillus_sp_C56T3:0.000002,WP_0837787791_Geobacillus_sp_C56T3:0.002737)90.6/99:0.005472,((ASS999421_Geobacillus_thermocatenulatus:0.000002,WP_0752614191_MULTISPECIES_Geobacillus:0.002760)94.2/99:0.005501,(RAN235251_Geobacillus_sp_A8:0.015191,KPC999151_Geobacillus_sp_BCO2:0.009984)0/22:0.000002)0/27:0.000002)49.8/88:0.002770,((EQB968041_Geobacillus_sp_A8:0.000002,((AGE216851_Geobacillus_sp_GHH01:0.000002,AMQ201481_Geobacillus_sp_JS12:0.002988)0/38:0.000002,((WP_0811324021_MULTISPECIES_Geobacillus:0.000002,WP_0816015221_Geobacillus_sp_GHH01:0.002752)0/36:0.000002,WP_1285779631_Geobacillus_sp_JS12:0.002743)83.7/50:0.002738)87.8/92:0.002747)0/38:0.000002,WP_0816532571_MULTISPECIES_Geobacillus:0.002736)91.9/95:0.005459)0/7:0.000002,KJE268501_Geobacillus_kaustophilus:0.002987)0/5:0.000002,(KZM546811_Geobacillus_stearothermophilus:0.000002,((AKU277021_Geobacillus_sp_LC300:0.005989,WP_1934440681_Geobacillus_stearothermophilus:0.002758)40.7/69:0.002762,(KZE962961_Geobacillus_stearothermophilus:0.000002,WP_1716979701_Geobacillus_sp_DSP4a:0.002762)97/100:0.011099)0/35:0.000002)97.3/98:0.010945)0/3:0.000002,ADU935951_Geobacillus_sp_Y412MC52:0.000002)0/7:0.000002,ALA691631_Geobacillus_stearothermophilus_10:0.002983)85.9/45:0.002777,(WP_0752617121_Geobacillus_kaustophilus:0.002749,WP_0837777811_Geobacillus_sp_Y412MC52:0.000002)0/19:0.000002)84.5/55:0.002783,WP_0962255251_Geobacillus_sp_FJAT46040:0.000002)93.2/94:0.005571,(WP_0811304621_MULTISPECIES_Geobacillus:0.000002,WP_0818231721_Geobacillus_sp_CAMR5420:0.002741)0/26:0.000002)0/21:0.000002,((((AEV187261_Geobacillus_thermoleovorans_CCB_US3_UF5:0.000002,WP_0752614311_MULTISPECIES_Geobacillus:0.002731)84.9/41:0.002723,KAF09956651_Geobacillus_sp_TFV3:0.002980)0/13:0.000002,KDE495291_Geobacillus_sp_CAMR5420:0.002980)0/9:0.000002,AMV104531_Geobacillus_thermoleovorans:0.000002)84.4/44:0.002731)83.7/71:0.002776,WP_0817126281_MULTISPECIES_Geobacillus:0.000002)87.6/96:0.007265,WP_0718801961_MULTISPECIES_Geobacillus:0.023760)42.3/86:0.005421,(OKO902581_FliI_Geobacillus_proteiniphilus:0.003011,WP_0740444211_MULTISPECIES_Geobacillus:0.000002)77.1/100:0.004503)84.9/87:0.009580,WP_0835099641_Geobacillus_jurassicus:0.019525)94.9/95:0.025731,((AKM185241_Geobacillus_sp_12AMOR1:0.000002,((ASS884511_Geobacillus_lituanicus:0.000002,(KAF65121801_FliI_Geobacillus_stearothermophilus:0.000002,((((KYD333211_B4114_0931_Geobacillus_stearothermophilus:0.003098,WP_1216253521_Geobacillus_stearothermophilus:0.002822)0/10:0.000002,WP_0811066221_Geobacillus_stearothermophilus:0.000002)82.8/76:0.002823,(WP_0807065331_MULTISPECIES_Geobacillus:0.000002,WP_0942398821_MULTISPECIES_unclassified_Geobacillus:0.002824)0/15:0.000002)88.7/13:0.002818,(OAO887381_FliI_Geobacillus_stearothermophilus:0.000002,WP_0812566801_Geobacillus_stearothermophilus:0.002818)42.1/90:0.002808)0/5:0.000002)84.1/59:0.003142)98.3/100:0.022736,STO117351_Probable_Flavobacterium_thermophilum:0.025940)67.5/93:0.013336)96.3/96:0.025658,KFL174451_Geobacillus_stearothermophilus:0.010421)94.5/98:0.020478)97.3/100:0.030350)84.6/95:0.024936)91.7/99:0.018765)0/55:0.000002);
	tree FliP = [&R] 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MBW26099141_Deltaproteobacteria_bacterium:0.159262)97.3/100:0.141547)82.1/98:0.096415)27/90:0.075046,MBN16275651_Deltaproteobacteria_bacterium:0.500793)95.1/100:0.140275,((KIX135171_Dethiosulfatarculus_sandiegensis:0.000002,WP_0824643381_Dethiosulfatarculus_sandiegensis:0.000002)97.3/100:0.167853,(KMY693151_Desulfocarbo_indianensis:0.006715,WP_0531114101_Desulfocarbo_indianensis:0.000002)99.2/100:0.245801)99.9/100:0.444112)98.5/100:0.218689,((HED011401_Proteobacteria_bacterium:0.053947,TSA091151_Deltaproteobacteria_bacterium:0.007696)100/100:0.343250,(((HFB834241_Thermodesulfatator_sp:0.000002,WP_1660328661_Thermosulfuriphilus_ammonigenes:0.000002)100/100:0.537669,HET983331_Desulfurivibrio_alkaliphilus:0.552794)28.1/85:0.039697,(MBW19802131_Deltaproteobacteria_bacterium:0.564489,(WP_1632988451_Dissulfurirhabdus_thermomarina:0.593372,MBW17116841_Deltaproteobacteria_bacterium:0.502264)80.7/96:0.143248)38.3/48:0.047439)92.2/94:0.094685)16.1/45:0.064724)58.8/85:0.033469,(MBI55840521_Deltaproteobacteria_bacterium:0.261319,(((MBM43073581_Deltaproteobacteria_bacterium:0.105960,MBM43391471_Deltaproteobacteria_bacterium:0.152081)94.4/100:0.070342,MBM43494281_Deltaproteobacteria_bacterium:0.017525)99.1/100:0.204438,OGP549061_Deltaproteobacteria_bacterium_RBG_13_52_11b:0.297813)95/100:0.172539)99.9/100:0.363556)92.5/98:0.073617)66.7/89:0.086566,(((HHA568801_Syntrophobacterales_bacterium:0.491069,((NTW069991_Syntrophaceae_bacterium:0.205666,OPY851891_precursor_Smithella_sp_PtaU1Bin162:0.095925)63.7/99:0.106583,PKN068791_Deltaproteobacteria_bacterium_HGWDeltaproteobacteria7:0.378558)98.9/100:0.278949)20/76:0.054336,MBP89813151_Syntrophobacterales_bacterium:0.308659)59.9/83:0.073168,(MBN15477811_Syntrophaceae_bacterium:0.195254,NLN591231_Deltaproteobacteria_bacterium:0.227944)99.6/100:0.318684)99.7/100:0.370739)91.4/100:0.129700)57.3/86:0.068896,(MBA30292331_Desulfobacteraceae_bacterium:0.000002,MBU43160241_Proteobacteria_bacterium:0.023001)100/100:0.744090)61.5/88:0.060059,(((((BBO667701_Desulfosarcina_alkanivorans:0.000002,WP_1553202941_Desulfosarcina_alkanivorans:0.000002)98.3/100:0.152822,WP_1553096141_Desulfosarcina_ovata:0.148150)99.8/100:0.294632,((KJS304241_Desulfatitalea_sp_BRH_c12:0.134312,RJQ848511_Desulfobacteraceae_bacterium:0.314898)65.9/100:0.090010,MBR99827991_Desulfatitalea_sp:0.310633)99.3/100:0.274345)93.4/91:0.109604,(VBB424861_flagellar_biosynthesis_protein_uncultured_Desulfatiglans_sp:0.473375,(MBC27528801_Desulfobacteraceae_bacterium:0.316739,MBL07160351_Desulfosarcina_sp:0.213570)99.2/100:0.262600)31.2/86:0.058759)15.2/71:0.022113,((HEN208561_Desulfobacteraceae_bacterium:0.032323,MBN12758521_Deltaproteobacteria_bacterium:0.006959)100/100:0.389204,(((((MBT94376701_Desulfobacterales_bacterium:0.192590,MBW19403831_Deltaproteobacteria_bacterium:0.167494)76.7/77:0.048093,(MBW17061031_Deltaproteobacteria_bacterium:0.140371,MBW27088271_Deltaproteobacteria_bacterium:0.030132)100/100:0.361265)69.8/75:0.036404,(MBW17406591_Deltaproteobacteria_bacterium:0.180936,MBW17007511_Deltaproteobacteria_bacterium:0.255701)83.8/99:0.047809)89.7/76:0.072329,MBW19012021_Deltaproteobacteria_bacterium:0.279808)85/97:0.083349,OQY160531_Desulfobacterium_sp_4572_20:0.325533)82.6/96:0.079197)88.9/99:0.121729)87/96:0.107963);
	tree MotA = [&R] 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end;