Phylogenetic analysis of peroxisomal proteins
(supplementary material for "Origin and evolution of the peroxisomal proteome". Gabaldon, T et. al. )

Below are the maximum likelihood trees as generated by PhyML for the Peroxisomal proteins. Trees were classified to be of a specific, prokaryotic origin when the Peroxisomal proteins are monophyletic with a specific bacterial taxon, e.g. alpha-proteobacteria (see Table 1). Homologs were detected by Smith-Waterman searches in completely sequenced genomes (E<0.01). Alignments were derived with Muscle. Protein names correspond to those of Table 1 (Sup. material), when the protein is present in both rat and mouse peroxisomal proteome only the yeast protein name is indicated. Sequence names are indicated by a name indicating the species source, followed by the sequence ID in the corresponding database. Trees of peroxisomal proteins with no prokaryotic homologs are ommitted.For each tree a graphic view is presented in .pdf format and in newick format. The latter can be viewed with several standard programs such as njplot and treeview

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AGT (tree_in_pdf)	(((((((X_axonopodis-Q8PM33:2.015812,((((((B_anthracis-Q81QF7:0.034382,B_cereus-Q81DG7:0.101014):1.06 0516,(((((P_aeruginosa-Q9I434:0.094591,P_putida-Q88KT0:0.088837):0.257650,R_meliloti-Q92UV9:0.311780 ):0.146546,(((((V_parahaemolyticus-Q87JL4:0.011749,V_vulnificus-Q8D3M4:0.003763):0.091988,V_cholerae -Q9KLY7:0.086483):0.063917,(S_typhimurium-P96060:0.004333,(S_typhi-Q8Z8W6:0.000000,S_enterica-Q8Z8W6 :0.000000):0.000000):0.242676):0.080889,(B_cereus-Q81G81:0.019837,B_anthracis-Q81TE0:0.016669):0.255 648):0.054727,L_plantarum-Q88YN9:0.371715):0.161625):0.129857,B_japonicum-Q9AMU5:0.720627):0.224885, (B_thetaiotaomicron-Q8A707:0.128052,C_tetani-Q893V7:0.156335):0.539324):0.256843):0.167555,((((((((( (((A_gambiae-SANGP00000019757:0.179504,D_melanogaster-Q9W3Z3:0.255849):0.117885,A_gambiae-SANGP00000 015996:0.308393):0.112217,C_elegans-Q94055:0.461627):0.053310,(((F_rubripens-SINFRUP00000069562:0.09 9927,D_rerio-ENSDARP00000021968:0.102329):0.056255,(D_rerio-ENSDARP00000017257:0.094300,F_rubripens- SINFRUP00000061293:0.087642):0.121389):0.079462,((M_musculus-IPI00314909.1:0.046059,R_norvergicus-AG T:0.013793):0.078910,H_sapiens-IPI00009367.1:0.096493):0.171482):0.182854):0.142640,(P_marinus-AAQ00 082:0.219961,Anabaena_sp.-Q8YY48:0.177405):0.161293):0.073595,((((((V_parahaemolyticus-Q87L98:0.0365 25,V_vulnificus-Q8DCJ5:0.050607):0.025847,V_cholerae-Q9KUW7:0.077570):0.093316,S_oneidensis-Q8E9E1:0 .103657):0.102226,M_magnetotacticum-C3855gene20:0.152474):0.044263,N_europaea-Q82Y54:0.223302):0.092 988,R_meliloti-Q92YP9:0.292006):0.200420):0.054785,(((B_subtilis-PUCG_BACSU:0.138179,B_halodurans-Q9 KET7:0.160800):0.050584,E_faecalis-Q82ZQ5:0.366089):0.099997,((X_axonopodis-Q8PQM3:0.033805,X_campes tris-Q8PDQ2:0.019229):0.167223,C_crescentus-Q9A560:0.136370):0.197239):0.275038):0.045310,D_radiodur ans-Q9RUN4:0.655594):0.089279,M_magnetotacticum-C3774gene4:0.674422):0.143403,((((C_acetobutylicum-Q 97N24:0.156615,C_perfringens-Q8XPB2:0.183749):0.403633,(P_abyssi-Q9V0F0:0.002342,(P_horikoshii-O5903 3:0.017947,P_furiosus-Q8U0V9:0.032510):0.022798):0.475072):0.228585,((((T_acidophilum-Q9HJF1:0.24571 0,T_volcanium-Q97B87:0.195359):0.353092,(S_tokodaii-Q974Q7:0.137317,S_solfataricus-Q97VM5:0.206931): 0.181876):0.242410,((C_albicans-CA0934:0.322676,N_crassa-NCU01821.1:0.309051):0.143666,(C_albicans-C A0935:0.149438,S_cerevisiae-YFD0_YEAST:0.372548):0.063250):0.341706):0.117534,A_pernix-Q9Y962:0.5062 89):0.081312):0.063877,((((M_thermoautotrophicum-O27638:0.257933,M_jannaschii-Q58369:0.304802):0.086 845,(M_kandleri-Q8TXM9:0.378023,(A_fulgidus-O28855:0.298961,((M_mazei-Q8Q091:0.030577,M_acetivorans- Q8TPT9:0.029782):0.188064,Halobacterium_sp.-Q9HMR6:0.637175):0.092833):0.111352):0.049602):0.066238, ((C_tetani-Q897N7:0.412880,T_tengcongensis-Q8R715:0.363786):0.143486,((((((R_meliloti-Q92XS6:0.19351 0,R_loti-Q98KU1:0.109006):0.181360,A_thaliana-O81248:0.291777):0.170695,(B_japonicum-Q89HF2:0.157828 ,B_japonicum-Q89HF4:0.224067):0.165931):0.086900,B_japonicum-Q89XE1:0.542618):0.262866,(((S_elongatu s-Q8DIW6:0.136720,Synechocystis_sp.-P74281:0.143445):0.085303,P_marinus-AAP99082:0.250511):0.184608, ((((S_aureus-Q99TE1:0.000000,S_aureus-Q99TE1:0.000000):0.000000,S_aureus-Q8NW43:0.002114):0.094168,S _epidermidis-Q8CS51:0.101443):0.379044,O_iheyensis-Q8EN62:0.339279):0.200673):0.060415):0.031890,((T _maritima-Q9X1C0:0.263961,C_tepidum-Q8KG98:0.472439):0.055645,(A_aeolicus-O67529:0.406945,((H_pylori -Y736_HELPJ:0.026740,H_pylori-Y736_HELPY:0.007481):0.269949,H_hepaticus-AAP77506:0.300730):0.440032) :0.224303):0.070406):0.064853):0.071504):0.047439,((((L_lactis-Q9CI76:0.186530,C_acetobutylicum-Q97M H7:0.195366):0.101374,C_perfringens-Q8XM36:0.272742):0.351235,P_aerophilum-Q8ZT41:0.478030):0.102959 ,(R_loti-Q988B8:0.518222,(S_avermitilis-Q829L2:0.430388,(A_tumefaciens-Q8UB00:0.000000,A_tumefaciens -Q8UB00:0.000000):0.449648):0.372722):0.213656):0.198226):0.050190):0.064879):0.076854,D_radiodurans -Q9RVN6:1.035638):0.085506,(P_aerophilum-Q8ZTC6:0.693848,(S_tokodaii-Q972B0:0.171660,S_solfataricus- Q97ZK0:0.171291):0.451894):0.242676):0.043410):0.085494,M_penetrans-Q8EUI8:1.007834):0.036276,D_radi odurans-Q9RRM3:1.190908):0.063656,((S_avermitilis-Q82GL4:0.050201,S_coelicolor-Q9F2Y1:0.073005):0.24 0219,B_longum-Q8G3U5:0.212125):1.214293):0.199076):0.225621,((P_abyssi-Q9UYT2:0.164405,P_horikoshii- O58360:0.109935):0.124984,P_furiosus-Q8U1Y8:0.210742):0.725074):0.342823,B_burgdorferi-CSD_BORBU:0.7 42517):0.075729,((E_faecalis-Q831E3:0.786137,T_tengcongensis-Q8R6L3:0.242760):0.179035,C_acetobutyli cum-Q97GL2:0.312641):0.222201):0.425217,W_glossinidia-Q8D2S0:0.640382):0.217145,R_conorii-Q92HP0:1.0 04661):0.580224,B_subtilis-O34599:0.050862,B_subtilis-CAB14693:0.025035);
ALDP (tree_in_pdf)	((((((((((M_penetrans-Q8EW56:5.418793,((S_avermitilis-Q82JJ0:0.437674,S_avermitilis-Q82II4:0.280648) :0.854329,R_solanacearum-Q8XY78:0.696533):2.144823):0.503287,(((((((((((ALDP:0.006658,M_musculus-IPI 00112111.1:0.000000):0.017144,H_sapiens-IPI00291373.1:0.017924):0.120803,(F_rubripens-SINFRUP0000007 4312:0.103290,((D_rerio-ENSDARP00000007052:0.071833,D_rerio-ENSDARP00000012155:0.000000):0.090525,D_ rerio-ENSDARP00000007526:0.092802):0.208143):0.050063):0.075963,((D_rerio-ENSDARP00000020546:0.36441 0,F_rubripens-SINFRUP00000073417:0.024598):0.029393,((R_norvergicus-IPI00213550.1:0.015681,M_musculu s-IPI00309437.2:0.000000):0.022499,H_sapiens-IPI00002618.1:0.000000):0.063531):0.069656):0.160554,(( D_melanogaster-Q8IMC0:0.000000,D_melanogaster-Q9V4B4:0.000000):0.124136,A_gambiae-SANGP00000019853:0 .115961):0.247268):0.038618,C_elegans-O45730:0.258271):0.338219,(N_crassa-NCU01751.1:0.363360,(C_alb icans-CA4993:0.492291,S_cerevisiae-PXA2_YEAST:0.643996):0.434512):0.152271):0.043288,(N_crassa-NCU08 382.1:0.417045,(C_albicans-CA5844:0.332904,S_cerevisiae-PXA1_YEAST:0.423048):0.398282):0.293632):0.1 41211,(((H_sapiens-IPI00002372.1:0.019159,((M_musculus-IPI00135646.1:0.000000,D_rerio-ENSDARP0000001 3511:0.155431):0.015571,(R_norvergicus-IPI00213729.1:0.093768,R_norvergicus-IPI00231860.2:0.000000): 0.007712):0.015747):0.231311,(C_elegans-Q18597:0.193213,C_elegans-Q18598:0.112780):0.174605):0.06097 9,(A_gambiae-SANGP00000020053:0.129597,D_melanogaster-Q9VWC8:0.097406):0.158900):0.470484):0.191869, A_thaliana-Q9SMR8:0.961408):0.259438,((((C_elegans-Q86S26:0.225617,C_elegans-O76414:0.000000):0.8992 49,C_elegans-Q18843:0.690637):0.135919,((D_rerio-ENSDARP00000021864:0.163390,F_rubripens-SINFRUP0000 0067042:0.178104):0.094740,((M_musculus-IPI00130626.1:0.010321,R_norvergicus-IPI00213834.1:0.007888) :0.032574,((H_sapiens-IPI00043176.2:0.031957,H_sapiens-IPI00184355.1:0.009483):0.000000,H_sapiens-IP I00023165.1:0.000000):0.036236):0.088707):0.488455):0.462903,(((((P_marinus-AAP99125:0.961939,Synech ocystis_sp.-Y182_SYNY3:0.246805):0.150373,S_elongatus-Q8DM98:0.400890):0.134339,(Anabaena_sp.-Q8YTQ0 :0.448062,Anabaena_sp.-Q8YTR3:0.306882):0.261363):0.095765,A_thaliana-Q9SLJ9:0.822713):0.203233,(((( (R_meliloti-O54061:0.330444,R_loti-Q98G04:0.285817):0.891461,((R_loti-Q98DC5:0.136294,(A_tumefaciens -Q8UBF6:0.000000,A_tumefaciens-Q8UBF6:0.000000):0.180577):0.072686,B_japonicum-Q89X10:0.118187):0.80 1186):0.268425,((P_syringae-Q87WJ5:0.465734,R_solanacearum-Q8Y280:0.499342):0.124744,B_japonicum-Q89 DA2:0.594579):0.033946):0.187154,(((H_influenzae-Y036_HAEIN:0.312158,P_multocida-Q9CLX7:0.272918):0. 258386,P_putida-Q88KQ0:0.464440):0.135934,H_influenzae-YE67_HAEIN:0.766005):0.296543):0.072518,(E_co li-YDDA_ECOLI:0.006549,E_coli-Q8FHG2:0.000233):1.219766):0.207188):0.457570):0.371507):0.419933):0.1 98553,(P_aeruginosa-Q9I2E0:2.427330,(X_campestris-Q8PAE1:1.656462,B_thetaiotaomicron-Q8A7I1:1.129257 ):0.819371):1.149761):0.317909,S_avermitilis-Q825G5:2.014005):0.299254,S_avermitilis-Q82FJ4:1.965142 ):0.412519,S_avermitilis-Q826H5:1.198842):0.200363,B_longum-Q8G7R8:1.502854):0.200264,V_vulnificus-Q 8D6P4:1.352458):0.256419,(M_musculus-IPI00261312.1:0.604548,H_sapiens-IPI00301976.1:1.550577):0.2356 32):0.775865,V_parahaemolyticus-Q87I14:0.058816,V_vulnificus-Q8D7H4:0.000000);
ALDPR (tree_in_pdf)	((((((((((M_penetrans-Q8EW56:5.418793,((S_avermitilis-Q82JJ0:0.437674,S_avermitilis-Q82II4:0.280648) :0.854329,R_solanacearum-Q8XY78:0.696533):2.144823):0.503287,(((((((((((ALDP:0.006658,M_musculus-IPI 00112111.1:0.000000):0.017144,H_sapiens-IPI00291373.1:0.017924):0.120803,(F_rubripens-SINFRUP0000007 4312:0.103290,((D_rerio-ENSDARP00000007052:0.071833,D_rerio-ENSDARP00000012155:0.000000):0.090525,D_ rerio-ENSDARP00000007526:0.092802):0.208143):0.050063):0.075963,((D_rerio-ENSDARP00000020546:0.36441 0,F_rubripens-SINFRUP00000073417:0.024598):0.029393,((R_norvergicus-IPI00213550.1:0.015681,M_musculu s-IPI00309437.2:0.000000):0.022499,H_sapiens-IPI00002618.1:0.000000):0.063531):0.069656):0.160554,(( D_melanogaster-Q8IMC0:0.000000,D_melanogaster-Q9V4B4:0.000000):0.124136,A_gambiae-SANGP00000019853:0 .115961):0.247268):0.038618,C_elegans-O45730:0.258271):0.338219,(N_crassa-NCU01751.1:0.363360,(C_alb icans-CA4993:0.492291,S_cerevisiae-PXA2_YEAST:0.643996):0.434512):0.152271):0.043288,(N_crassa-NCU08 382.1:0.417045,(C_albicans-CA5844:0.332904,S_cerevisiae-PXA1_YEAST:0.423048):0.398282):0.293632):0.1 41211,(((H_sapiens-IPI00002372.1:0.019159,((M_musculus-IPI00135646.1:0.000000,D_rerio-ENSDARP0000001 3511:0.155431):0.015571,(R_norvergicus-IPI00213729.1:0.093768,R_norvergicus-IPI00231860.2:0.000000): 0.007712):0.015747):0.231311,(C_elegans-Q18597:0.193213,C_elegans-Q18598:0.112780):0.174605):0.06097 9,(A_gambiae-SANGP00000020053:0.129597,D_melanogaster-Q9VWC8:0.097406):0.158900):0.470484):0.191869, A_thaliana-Q9SMR8:0.961408):0.259438,((((C_elegans-Q86S26:0.225617,C_elegans-O76414:0.000000):0.8992 49,C_elegans-Q18843:0.690637):0.135919,((D_rerio-ENSDARP00000021864:0.163390,F_rubripens-SINFRUP0000 0067042:0.178104):0.094740,((M_musculus-IPI00130626.1:0.010321,R_norvergicus-IPI00213834.1:0.007888) :0.032574,((H_sapiens-IPI00043176.2:0.031957,H_sapiens-IPI00184355.1:0.009483):0.000000,H_sapiens-IP I00023165.1:0.000000):0.036236):0.088707):0.488455):0.462903,(((((P_marinus-AAP99125:0.961939,Synech ocystis_sp.-Y182_SYNY3:0.246805):0.150373,S_elongatus-Q8DM98:0.400890):0.134339,(Anabaena_sp.-Q8YTQ0 :0.448062,Anabaena_sp.-Q8YTR3:0.306882):0.261363):0.095765,A_thaliana-Q9SLJ9:0.822713):0.203233,(((( (R_meliloti-O54061:0.330444,R_loti-Q98G04:0.285817):0.891461,((R_loti-Q98DC5:0.136294,(A_tumefaciens -Q8UBF6:0.000000,A_tumefaciens-Q8UBF6:0.000000):0.180577):0.072686,B_japonicum-Q89X10:0.118187):0.80 1186):0.268425,((P_syringae-Q87WJ5:0.465734,R_solanacearum-Q8Y280:0.499342):0.124744,B_japonicum-Q89 DA2:0.594579):0.033946):0.187154,(((H_influenzae-Y036_HAEIN:0.312158,P_multocida-Q9CLX7:0.272918):0. 258386,P_putida-Q88KQ0:0.464440):0.135934,H_influenzae-YE67_HAEIN:0.766005):0.296543):0.072518,(E_co li-YDDA_ECOLI:0.006549,E_coli-Q8FHG2:0.000233):1.219766):0.207188):0.457570):0.371507):0.419933):0.1 98553,(P_aeruginosa-Q9I2E0:2.427330,(X_campestris-Q8PAE1:1.656462,B_thetaiotaomicron-Q8A7I1:1.129257 ):0.819371):1.149761):0.317909,S_avermitilis-Q825G5:2.014005):0.299254,S_avermitilis-Q82FJ4:1.965142 ):0.412519,S_avermitilis-Q826H5:1.198842):0.200363,B_longum-Q8G7R8:1.502854):0.200264,V_vulnificus-Q 8D6P4:1.352458):0.256419,(M_musculus-IPI00261312.1:0.604548,H_sapiens-IPI00301976.1:1.550577):0.2356 32):0.775865,V_parahaemolyticus-Q87I14:0.058816,V_vulnificus-Q8D7H4:0.000000);
AMCR (tree_in_pdf)	(((((((((((((((B_japonicum-Q89Q27:0.312304,R_loti-Q98LH6:0.433435):0.219089,(R_meliloti-Q92VN1:0.296 496,R_loti-Q986Y6:0.073386):0.467520):0.076197,S_coelicolor-Q9RJU8:0.510969):0.166094,((B_japonicum- Q89GF2:0.178731,P_putida-Q88IJ8:0.200849):0.377433,B_japonicum-Q89RJ3:0.621569):0.099614):0.071091,( ((((S_coelicolor-O87838:0.016859,S_avermitilis-Q82M40:0.025565):0.183388,(B_japonicum-Q89QH2:0.14715 4,((E_coli-Q8XBR7:0.000000,E_coli-Q8XBR7:0.000000):0.000000,((E_coli-YFDW_ECOLI:0.000000,S_flexneri- YFDW_ECOLI:0.000000):0.000000,(S_flexneri-YFDW_ECOLI:0.000000,E_coli-Q8FFE8:0.000000):0.000000):0.00 0000):0.280139):0.076744):0.476592,((C_tetani-Q892K9:0.381776,(((S_flexneri-Q83QP5:0.000000,(S_flexn eri-AAP17759:0.000000,(E_coli-Q8XCJ8:0.009914,E_coli-Q8XCJ8:0.000000):0.012282):0.009081):0.006744,E _coli-Q8FFF0:0.004484):0.009779,E_coli-YFDE_ECOLI:0.006252):0.450997):0.065434,B_japonicum-Q89GG5:0. 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ECI1 (tree_in_pdf)	((((((((((((M_musculus-IPI00318283.1:0.09272,F_rubripens-SINFRUP00000071210:0.22209):0.01645,H_sapie ns-IPI00256376.1:0.04179):0.17263,C_elegans-Q20184:0.33636):0.11140,A_fulgidus-O28632:0.35853):0.529 38,((((R_loti-Q98AG1:0.20957,R_loti-Q98AB8:0.19298):0.34407,S_avermitilis-Q82Q04:0.29210):0.16461,(( S_enterica-CAID_SALTI:0.00000,S_typhi-CAID_SALTI:0.00000):0.00000,S_typhimurium-CAID_SALTY:0.00000): 0.43277):0.03930,(R_loti-Q98CR0:0.50956,(((M_bovis-CAD94035:0.00000,M_tuberculosis-O06542:0.00000):0 .00000,M_tuberculosis-O06542:0.00000):0.67547,M_magnetotacticum-C3822gene16:0.74928):0.04743):0.0951 5):0.03799):0.06869,((C_elegans-Q20376:0.30969,P_aeruginosa-Q9HYH9:0.24477):0.53096,(B_japonicum-Q89 R26:0.48613,A_thaliana-O23468:0.80372):0.06898):0.00921):0.05245,((((((B_japonicum-Q89IN0:0.13693,C_ crescentus-Q9A9M9:0.23532):0.50489,B_japonicum-Q89R20:0.58377):0.04499,(((M_bovis-ECHE_MYCTU:0.00000 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ERG1 (tree_in_pdf)	(((((((((((H_sapiens-gi1483186dbjBAA11209.1:0.002926,H_sapiens-ERG1:0.012482):0.000000,H_sapiens-gi6 2865635refNP_003120.2:0.000000):0.000000,H_sapiens-gi57997512embCAI46076.1:0.004981):0.042140,((M_mu sculus-gi74183459dbjBAE36598.1:0.000000,M_musculus-gi33990042gbAAH56361.1:0.000000):0.027300,R_norve rgicus-gi8394354refNP_058832.1:0.057232):0.080752):0.149036,D_rerio-gi68403773refXP_693698.1:0.26992 6):0.298637,(((A_thaliana-gi15237902refNP_197803.1:0.058219,A_thaliana-gi15237903refNP_197804.1:0.08 7554):0.123394,A_thaliana-SQP2:0.225912):0.443930,((((A_thaliana-gi7270759embCAB80441.1:0.000000,A_t haliana-gi18420113refNP_568033.1:0.000000):0.000000,A_thaliana-gi21537043gbAAM61384.1:0.002487):0.08 9969,A_thaliana-gi15227757refNP_179868.1:0.080809):0.083919,(A_thaliana-gi12321049gbAAG50645.1AC0826 :0.000000,A_thaliana-gi18406296refNP_564734.1:0.000000):0.135367):0.144949):0.400436):0.248892,N_cra ssa-gi32417016refXP_328986.1:0.628140):0.046372,(S_pombe-gi12311756:0.597100,(C_albicans-gi68488479: 0.356677,S_cerevisiae-ERG1:0.505487):0.329237):0.117357):0.919770,M_tuberculosis-gi2131016embCAB0931 7.1:2.636010):0.352572,(V_vulnificus-gi37197844dbjBAC93682.1:0.880096,V_cholerae-gi75829334refZP_007 58641.1:1.077570):2.129868):1.737111,P_aeruginosa-gi9950400gbAAG07577.1AE00483:0.027077,P_aeruginosa -gi32039405refZP_00137677.1:0.006936);
ERG6 (tree_in_pdf)	((((R_solanacearum-83746433:0.005603,R_solanacearum-17430641:0.078031):1.291569,(Anabaena_sp.-316167 31:1.859951,((C_elegans-gi16950435:1.370777,((((((S_pombe-41688402:0.018176,S_pombe-gi19112579:0.011 901):0.355053,N_crassa-ERG6:0.236254):0.068123,(C_albicans-gi68468538:0.225330,S_cerevisiae-ERG6:0.2 33826):0.107050):0.179114,A_thaliana-SMT1:0.423054):0.067710,(((A_thaliana-22136020:0.000000,A_thali ana-SMT2:0.000000):0.000000,A_thaliana-1061040:0.003976):0.046248,A_thaliana-SMT3:0.103571):0.681346 ):0.213122,N_crassa-32422515:1.549738):0.082565):0.247187,(R_meliloti-gi14023914:1.669339,(((S_averm itilis-gi29604577:0.943275,((Synechocystis_sp.-1653572:0.081153,Anabaena_sp.-75701026:0.150931):0.15 0386,P_marinus-72002759:0.462345):0.919153):0.256668,B_cereus-29898677:1.642125):0.022034,(R_melilot i-14026530:0.710834,R_meliloti-14022360:0.705639):0.747310):0.222366):0.046094):0.111791):0.173922): 0.325283,(P_abyssi-5457639:0.236583,P_furiosus-18892058:0.129973):0.914584):1.638275,B_suis-23464445 :0.009115,B_melitensis-17984376:0.000000);
FAA2 (tree_in_pdf)	(((((((((((((M_tuberculosis-O05598:0.000000,M_bovis-CAD93901:0.028694):0.016384,M_tuberculosis-O0559 8:0.010726):1.303938,C_burnetii-Q83AH1:0.806324):0.188647,(((S_avermitilis-Q93GZ6:0.928007,(Anabaena _sp.-Q8YTN6:0.685493,P_syringae-Q87WM8:0.921779):0.160714):0.168591,(A_tumefaciens-Q8U9Q3:0.104934,A _tumefaciens-Q8U9Q3:0.076619):0.744662):0.155267,(M_tuberculosis-P96290:0.040359,(M_tuberculosis-P96 290:0.000000,M_bovis-CAD96653:0.004746):0.067449):1.236350):0.201355):0.198368,(B_subtilis-PKSJ_BACS U:0.871141,R_solanacearum-Q8XQ67:0.889471):0.751602):0.302406,(((((((((S_typhi-CAIC_SALTI:0.077443,S _enterica-CAIC_SALTI:0.034825):1.182667,D_radiodurans-Q9RYK3:1.121738):0.211312,((((((R_solanacearum -Q8Y294:0.208448,R_loti-Q987S7:0.184577):0.142120,S_oneidensis-Q8EFK0:0.369372):0.067409,((((F_rubri pens-SINFRUP00000081571:0.271281,F_rubripens-SINFRUP00000052794:0.461667):0.096982,(M_musculus-IPI00 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FAT2 (tree_in_pdf)	((((((((((((M_musculus-IPI00318283.1:0.09272,F_rubripens-SINFRUP00000071210:0.22209):0.01645,H_sapie ns-IPI00256376.1:0.04179):0.17263,C_elegans-Q20184:0.33636):0.11140,A_fulgidus-O28632:0.35853):0.529 38,((((R_loti-Q98AG1:0.20957,R_loti-Q98AB8:0.19298):0.34407,S_avermitilis-Q82Q04:0.29210):0.16461,(( S_enterica-CAID_SALTI:0.00000,S_typhi-CAID_SALTI:0.00000):0.00000,S_typhimurium-CAID_SALTY:0.00000): 0.43277):0.03930,(R_loti-Q98CR0:0.50956,(((M_bovis-CAD94035:0.00000,M_tuberculosis-O06542:0.00000):0 .00000,M_tuberculosis-O06542:0.00000):0.67547,M_magnetotacticum-C3822gene16:0.74928):0.04743):0.0951 5):0.03799):0.06869,((C_elegans-Q20376:0.30969,P_aeruginosa-Q9HYH9:0.24477):0.53096,(B_japonicum-Q89 R26:0.48613,A_thaliana-O23468:0.80372):0.06898):0.00921):0.05245,((((((B_japonicum-Q89IN0:0.13693,C_ crescentus-Q9A9M9:0.23532):0.50489,B_japonicum-Q89R20:0.58377):0.04499,(((M_bovis-ECHE_MYCTU:0.00000 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0.15578,((D_radiodurans-Q9RRI1:0.40648,((C_crescentus-Q9A775:0.14061,B_japonicum-Q89R29:0.29339):0.1 7502,B_japonicum-Q89T20:0.33662):0.05709):0.05459,S_avermitilis-Q82GR8:0.33824):0.05978):0.08649):0. 03886,(((((M_bovis-CAD93327:0.00000,M_tuberculosis-O07179:0.00000):0.00000,M_tuberculosis-O07179:0.0 0000):1.13151,((M_bovis-CAD94672:0.00000,M_tuberculosis-P95279:0.00000):0.00000,M_tuberculosis-P9527 9:0.00000):0.83848):0.11757,B_japonicum-Q89RE2:0.92301):0.10884,(B_japonicum-Q89C96:0.48606,B_japoni cum-Q89Y12:0.51774):0.13980):0.10282):0.03297,((((M_tuberculosis-ECHC_MYCTU:0.00000,M_tuberculosis-E CHC_MYCTU:0.00000):0.00000,M_bovis-CAD96174:0.00000):0.38396,D_radiodurans-Q9RXX1:0.71701):0.18225,( B_japonicum-Q89WX6:0.54648,B_japonicum-Q89CE0:0.83112):0.17048):0.04569):0.03943):0.02209,(C_crescen tus-Q9A582:0.53902,C_efficiens-Q8FRT6:0.79367):0.14645):0.07772):0.07461,(((((((((A_gambiae-SANGP000 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_oneidensis-Q8EGC4:0.12381):0.06962):0.01066,P_aeruginosa-Q9I5I4:0.17543):0.26945,(R_meliloti-Q92KZ5 :0.13292,B_suis-Q8FY43:0.14136):0.39598):0.04861):0.00933,((((((S_solfataricus-Q97VU5:0.10376,S_toko daii-Q976X0:0.09517):0.07246,A_pernix-Q9YBW6:0.22326):0.08580,(S_tokodaii-Q970T6:0.11588,S_solfatari cus-Q9UX44:0.27137):0.12472):0.05585,(B_halodurans-Q9KBD2:0.34130,A_fulgidus-O30218:0.44506):0.03854 ):0.03756,(L_interrogans-Q8F6V2:0.39902,((B_halodurans-Q9KDS6:0.20270,L_interrogans-Q8F9W4:0.47057): 0.13670,B_anthracis-Q81YG6:0.25374):0.08680):0.01192):0.01662,(((((B_cereus-Q817L6:0.04222,B_anthrac is--Q81L70:0.00455):0.21873,B_halodurans-Q9K8A5:0.18071):0.04685,O_iheyensis-Q8EPI5:0.31429):0.04103 ,B_subtilis-P94549:0.18852):0.08456,((D_radiodurans-Q9RUA4:0.38352,(D_rerio-ENSDARP00000007689:0.126 38,F_rubripens-SINFRUP00000086414:0.02607):0.47309):0.02972,B_japonicum-Q89CH6:0.31676):0.22245):0.0 8100):0.01884,:0.54208)TRICHOTOMY;
FOX1 (tree_in_pdf)	((((((((((((((((H_sapiens-IPI00296907.1:0.010695,H_sapiens-IPI00296906.1:0.073213):0.037190,((R_norv ergicus-IPI00200540.1:0.017713,(R_norvergicus-IPI00231941.1:0.000000,M_musculus-IPI00224080.1:0.1993 30):0.000000):0.012531,(R_norvergicus-IPI00211510.1:0.000000,M_musculus-IPI00127558.1:0.027902):0.06 6572):0.047793):0.261666,(((C_elegans-Q9XV65:0.500521,((((C_elegans-O62139:0.107616,C_elegans-O62138 :0.122110):0.036376,C_elegans-O62137:0.153526):0.111463,C_elegans-O62140:0.163293):0.196257,C_elegan s-CAOP_CAEEL:0.589055):0.125245):0.078348,C_elegans-Q93839:0.323011):0.213346,((D_melanogaster-Q9W2G 9:0.423661,D_melanogaster-Q9W2G8:0.376469):0.221871,(((A_gambiae-SANGP00000020032:0.092106,A_gambiae -SANGP00000020118:0.179082):0.159114,D_melanogaster-Q9W3U0:0.591273):0.033390,D_melanogaster-Q9Y130: 0.215285):0.140541):0.242601):0.150262):0.135089,((R_norvergicus-IPI00205561.1:0.063518,M_musculus-I PI00134870.1:0.082690):0.156082,H_sapiens-IPI00293125.1:0.160157):0.565492):0.182615,(A_thaliana-Q9Z QP2:0.115636,A_thaliana-O23518:0.049433):0.379396):0.321523,(S_cerevisiae-CAO_YEAST:0.304428,(C_albi cans-CA1574:0.416669,(C_albicans-CA2051:0.273934,C_albicans-CA1572:0.106567):0.078884):0.122451):0.7 11479):0.238491,(((((H_sapiens-IPI00165063.1:0.000000,H_sapiens-IPI00020226.1:0.003073):0.127593,((R _norvergicus-IPI00209045.1:0.017273,R_norvergicus-IPI00199643.1:0.113941):0.044897,(M_musculus-IPI00 336393.1:0.000000,M_musculus-IPI00318108.1:0.012284):0.045874):0.083689):0.150683,F_rubripens-SINFRU P00000080445:0.142408):0.240255,(((A_gambiae-SANGP00000010039:0.235292,A_gambiae-SANGP00000010603:0. 657878):0.173163,D_melanogaster-Q9VMD7:0.344557):0.240450,(A_gambiae-SANGP00000011863:0.217459,D_mel anogaster-Q9VIX4:0.128758):0.403668):0.083953):0.085025,C_elegans-Q20992:0.736608):0.239494):0.18744 6,((A_thaliana-Q9FJQ4:0.612752,(A_thaliana-Q9LMI8:0.067438,A_thaliana-Q9LMI7:0.023084):0.726175):0.0 61846,(((R_norvergicus-IPI00209296.1:0.693212,M_musculus-IPI00120087.1:0.019856):0.020878,R_norvergi cus-IPI00211367.1:0.210010):0.263828,H_sapiens-IPI00185171.1:0.210190):0.594493):0.095211):0.269770, (S_avermitilis-Q82H40:1.398310,S_coelicolor-Q9Z4Y4:1.547844):0.197684):0.968969,(C_efficiens-Q8FSQ8: 0.195446,C_efficiens-Q8CWF0:0.248606):0.752605):0.541484,(((S_coelicolor-Q9S251:0.039514,S_avermitil is-Q828R2:0.026750):0.597945,A_gambiae-SANGP00000020214:0.726362):0.107629,((Halobacterium_sp.-Q9HRI 6:0.452181,Halobacterium_sp.-Q9HPT2:0.592295):0.203892,((((R_norvergicus-IPI00231359.2:0.004001,M_mu sculus-IPI00331251.1:0.001898):0.045522,H_sapiens-IPI00027701.1:0.044718):0.101389,D_melanogaster-Q9 VDT1:0.213687):0.382489,(O_iheyensis-Q8EM49:0.412875,(F_nucleatum-Q8R5V8:0.386301,D_radiodurans-Q9RU 50:0.749150):0.080834):0.048689):0.046619):0.070030):0.117967):0.060073,((((M_magnetotacticum-C3735g ene3:0.132203,B_suis-Q8FX67:0.231921):0.073557,(C_crescentus-Q9A7C6:0.144279,C_crescentus-Q9AB07:0.0 58257):0.229649):0.359968,D_radiodurans-Q9RVV0:0.711447):0.149234,V_parahaemolyticus-Q87II4:0.819718 ):0.127464):0.185739,(D_melanogaster-Q9V8T1:0.416701,M_musculus-IPI00331710.1:0.387225):0.560139):0. 338987,B_subtilis-O32176:0.339474):0.151771,O_iheyensis-Q8ES29:0.328097):0.168660,B_anthracis-Q81QR7 :0.015044,B_cereus-Q81DR7:0.000000);
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GPD1 (tree_in_pdf)	((((((((((((M_musculus-IPI00318283.1:0.09272,F_rubripens-SINFRUP00000071210:0.22209):0.01645,H_sapie ns-IPI00256376.1:0.04179):0.17263,C_elegans-Q20184:0.33636):0.11140,A_fulgidus-O28632:0.35853):0.529 38,((((R_loti-Q98AG1:0.20957,R_loti-Q98AB8:0.19298):0.34407,S_avermitilis-Q82Q04:0.29210):0.16461,(( S_enterica-CAID_SALTI:0.00000,S_typhi-CAID_SALTI:0.00000):0.00000,S_typhimurium-CAID_SALTY:0.00000): 0.43277):0.03930,(R_loti-Q98CR0:0.50956,(((M_bovis-CAD94035:0.00000,M_tuberculosis-O06542:0.00000):0 .00000,M_tuberculosis-O06542:0.00000):0.67547,M_magnetotacticum-C3822gene16:0.74928):0.04743):0.0951 5):0.03799):0.06869,((C_elegans-Q20376:0.30969,P_aeruginosa-Q9HYH9:0.24477):0.53096,(B_japonicum-Q89 R26:0.48613,A_thaliana-O23468:0.80372):0.06898):0.00921):0.05245,((((((B_japonicum-Q89IN0:0.13693,C_ crescentus-Q9A9M9:0.23532):0.50489,B_japonicum-Q89R20:0.58377):0.04499,(((M_bovis-ECHE_MYCTU:0.00000 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_oneidensis-Q8EGC4:0.12381):0.06962):0.01066,P_aeruginosa-Q9I5I4:0.17543):0.26945,(R_meliloti-Q92KZ5 :0.13292,B_suis-Q8FY43:0.14136):0.39598):0.04861):0.00933,((((((S_solfataricus-Q97VU5:0.10376,S_toko daii-Q976X0:0.09517):0.07246,A_pernix-Q9YBW6:0.22326):0.08580,(S_tokodaii-Q970T6:0.11588,S_solfatari cus-Q9UX44:0.27137):0.12472):0.05585,(B_halodurans-Q9KBD2:0.34130,A_fulgidus-O30218:0.44506):0.03854 ):0.03756,(L_interrogans-Q8F6V2:0.39902,((B_halodurans-Q9KDS6:0.20270,L_interrogans-Q8F9W4:0.47057): 0.13670,B_anthracis-Q81YG6:0.25374):0.08680):0.01192):0.01662,(((((B_cereus-Q817L6:0.04222,B_anthrac is--Q81L70:0.00455):0.21873,B_halodurans-Q9K8A5:0.18071):0.04685,O_iheyensis-Q8EPI5:0.31429):0.04103 ,B_subtilis-P94549:0.18852):0.08456,((D_radiodurans-Q9RUA4:0.38352,(D_rerio-ENSDARP00000007689:0.126 38,F_rubripens-SINFRUP00000086414:0.02607):0.47309):0.02972,B_japonicum-Q89CH6:0.31676):0.22245):0.0 8100):0.01884,:0.54208)TRICHOTOMY;
GTK1 (tree_in_pdf)	((((((C_elegans-Q22312:2.350357,((N_crassa-NCU01636.1:1.390244,(((R_solanacearum-Q8Y2R2:0.553767,M_m agnetotacticum-C3723gene13:0.617152):0.497266,(B_japonicum-Q89IM8:0.747340,(P_putida-Q88IW7:0.350358 ,(P_aeruginosa-Q9I714:0.253048,(C_crescentus-Q9AAF8:0.437563,B_japonicum-Q89WU0:0.592015):0.511772): 0.062890):0.461263):0.105053):0.397677,N_crassa-NCU06494.1:1.158541):0.095643):0.245367,(C_elegans-Y S21_CAEEL:0.829811,C_elegans-YYS7_CAEEL:0.875719):0.132361):0.159293):0.288451,F_rubripens-SINFRUP00 000072155:0.213151):0.056675,D_rerio-ENSDARP00000017846:0.452450):0.395425,H_sapiens-IPI00219673.1:0 .144905):0.167862,M_musculus-IPI00121051.1:0.061953):0.016435,R_norvergicus-GTK1:0.080741,M_musculus -IPI00138258.1:0.183781);
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NPY1 (tree_in_pdf)	((((C_acetobutylicum-Q97D79:5.822382,(((L_plantarum-Q88T63:1.626860,(((B_thetaiotaomicron-Q8A7I0:0.8 67704,C_burnetii-Q83CZ6:0.856173):0.201152,((M_acetivorans-Q8TQV0:0.093975,M_mazei-Q8PU15:0.040498): 0.452737,C_acetobutylicum-Q97DS6:0.684739):0.082638):0.189427,(((((P_multocida-NUDC_PASMU:0.187575,H _influenzae-NUDC_HAEIN:0.252487):0.382600,((((E_coli-NUDC_ECOLI:0.004549,((S_flexneri-Q83IS3:0.00000 0,S_flexneri-AAP18704:0.000000):0.004505,(E_coli-NUDC_ECO57:0.000000,E_coli-NUDC_ECO57:0.000000):0.0 04499):0.004449):0.004415,E_coli-NUDC_ECOL6:0.004583):0.040880,(S_typhimurium-NUDC_SALTY:0.004160,(S _typhi-NUDC_SALTI:0.000000,S_enterica-NUDC_SALTI:0.000000):0.009215):0.038388):0.084417,(Y_pestis-NU DC_YERPE:0.000000,Y_pestis-NUDC_YERPE:0.000000):0.178262):0.370564):0.114701,((V_parahaemolyticus-NU DC_VIBPA:0.172738,V_vulnificus-NUDC_VIBVU:0.157668):0.070393,V_cholerae-NUDC_VIBCH:0.102400):0.63464 2):0.381219,D_radiodurans-NUDC_DEIRA:0.597618):0.153402,((P_syringae-Q882A9:0.221056,P_putida-Q88FQ8 :0.152781):0.139909,P_aeruginosa-NUDC_PSEAE:0.215264):0.585860):0.221697):0.207688):0.288180,((C_tet ani-Q899U7:1.508476,C_perfringens-Q8XMD4:1.123042):1.545153,(C_elegans-NAPY_CAEEL:1.095298,R_solanac earum-Q8Y181:1.634124):0.119961):0.339259):0.084211,((((X_campestris-Q8PD56:0.077057,X_axonopodis-Q8 PQ29:0.046663):0.827050,S_avermitilis-Q82IQ9:0.516447):0.211717,M_magnetotacticum-C3612gene2:0.82324 9):0.000000,(((((F_rubripens-SINFRUP00000088784:0.320117,D_rerio-ENSDARP00000022861:0.419228):0.1123 42,(M_musculus-IPI00121076.1:0.015591,H_sapiens-IPI00027778.1:0.044323):0.093956):0.373344,((N_crass a-NCU00293.1:0.517023,(C_albicans-CA2897:0.517924,S_cerevisiae-NAPY_YEAST:0.593375):0.397301):0.1927 46,S_pombe-NAPY_SCHPO:0.641441):0.207288):0.069833,(((M_musculus-IPI00330451.1:0.005136,M_musculus-I PI00110522.1:0.000000):0.117726,H_sapiens-IPI00003191.3:0.112943):0.168641,D_rerio-ENSDARP0000002485 2:0.571802):0.541863):0.162297,((B_japonicum-Q89BM5:0.438912,C_crescentus-Q9ABG1:0.611939):0.234884, (((B_melitensis-Q8YEH2:0.040334,B_suis-Q8G3B4:0.004153):0.441221,((A_tumefaciens-Q8UJ40:0.000000,A_t umefaciens-Q8UJ40:0.000000):0.238299,R_meliloti-Q92KT4:0.209261):0.430260):0.087068,R_loti-Q98BN0:0. 229815):0.280686):0.088356):0.218018):0.150403):0.104389):0.000000,B_longum-Q8G4Z6:1.165762):0.87218 8,M_bovis-CAD95316:0.000000):0.000000,M_tuberculosis-NUDC_MYCTU:0.000000,M_tuberculosis-NUDC_MYCTU:0 .000000);
PAHX (tree_in_pdf)	((((((((R_solanacearum-Q8XTA5:1.584605,S_avermitilis-Q829L6:1.672225):0.406852,H_hepaticus-CAD75424: 1.420628):0.113824,R_loti-Q986A6:1.935608):0.071466,((((((((A_gambiae-SANGP00000012829:0.003995,A_ga mbiae-SANGP00000010487:0.009682):0.261156,D_melanogaster-Q9VGY8:0.242331):0.378963,C_elegans-Q9NAM7: 0.553800):0.084914,(((D_rerio-ENSDARP00000016229:0.063825,D_rerio-ENSDARP00000015072:0.001477):0.171 804,F_rubripens-SINFRUP00000070154:0.194715):0.099867,(R_norvergicus-IPI00212998.1:0.009976,M_muscul us-IPI00118997.1:0.030634):0.297132):0.197651):0.102864,A_thaliana-Q9ZVF6:0.572354):0.093211,(N_cras sa-NCU04228.1:0.451147,C_albicans-CA5552:0.427292):0.252516):0.727621,B_cereus-Q815P9:1.441782):0.10 4561,R_loti-Q98AN1:1.965082):0.207001):0.179757,((C_elegans-O62514:0.380349,(C_elegans-PAHX_CAEEL:0. 105421,((D_rerio-ENSDARP00000026922:0.261713,F_rubripens-SINFRUP00000062833:0.112407):0.043682,((M_m usculus-IPI00129963.1:0.063110,R_norvergicus-IPI00192572.1:0.057893):0.060292,H_sapiens-IPI00219655. 1:0.059861):0.091944):0.276815):0.029807):0.519748,Anabaena_sp.-Q8YNY2:1.757254):0.376139):0.146865, X_axonopodis-Q8PGL9:2.390494):2.418143,M_bovis-Y0D3_MYCTU:0.000000):0.000000,M_tuberculosis-Y0D3_MYC TU:0.000000,M_tuberculosis-Y0D3_MYCTU:0.000000);
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PNC1 (tree_in_pdf)	((((((((((T_pallidum-O83694:1.541224,C_jejuni-Q9PJ08:1.489277):0.575559,((B_japonicum-Q89CT5:2.84638 8,((((((((S_agalactiae-Q8E3N8:0.005148,S_agalactiae-Q8DY19:0.000000):0.126847,(S_mutans-Q8DSG2:0.051 314,(S_pneumoniae-Q8DP02:0.000000,S_pneumoniae-Q97PM2:0.000000):0.193307):0.054927):0.078261,((S_pyo genes-Q99YB8:0.000000,S_pyogenes-Q99YB8:0.000000):0.000000,(S_pyogenes-Q8K615:0.000000,S_pyogenes-Q8 K615:0.000000):0.005450):0.210545):0.153946,E_faecalis-Q82Z79:0.145129):0.113372,L_plantarum-Q88U99: 0.364877):0.047088,(((B_cereus-Q81DY3:0.148052,O_iheyensis-Q8ESQ6:0.123940):0.070867,B_halodurans-Q9 K6F2:0.321015):0.018719,B_subtilis-O32091:0.197774):0.043449):0.081149,(((S_aureus-Q99SW9:0.000000,S _aureus-Q99SW9:0.000000):0.000000,S_aureus-Q99SW9:0.000000):0.180680,S_epidermidis-Q8CNN8:0.174018): 0.306668):0.614157,(((M_kandleri-Q8TY03:0.538027,T_maritima-Q9WYU6:0.639169):0.089722,((P_syringae-Q 881B5:1.126825,B_anthracis-Q81P55:1.163517):0.317452,C_perfringens-Q8XMU9:1.324554):0.169214):0.0391 59,(((((A_pernix-Q9Y9D7:0.240907,P_aerophilum-Q8ZU08:0.230240):0.100544,(S_solfataricus-Q97VZ5:0.157 339,S_tokodaii-Q974T0:0.077171):0.183028):0.165853,Halobacterium_sp.-Q9HMH5:0.965142):0.168673,(T_ac idophilum-Q9HKY9:0.290499,T_volcanium-Q97AM6:0.220603):0.523265):0.163733,A_fulgidus-O28131:0.388887 ):0.092050):0.094340):0.113036):0.077036,N_crassa-NCU05807.1:1.483157):0.077312):0.189193,(C_tetani- Q897N3:1.132947,(((C_efficiens-Q8FMW4:0.108526,C_glutamicum-Q8NMS8:0.209724):0.306269,(((S_avermitil is-Q82D30:0.028802,S_coelicolor-Q9S2G3:0.026879):0.196345,(M_bovis-CAD96922:0.005152,(M_tuberculosis -Q50575:0.000000,M_tuberculosis-Q50575:0.000000):0.000000):0.209472):0.097721,B_longum-Q8G5V5:0.6918 40):0.067324):0.201524,(T_whipplei-Q83FM5:0.000000,T_whipplei-Q83N93:0.000000):0.596117):0.322541):0 .081070):0.053979,(((P_abyssi-Q9V015:0.014668,P_horikoshii-O58727:0.070102):0.032481,P_furiosus-Q8U1 V0:0.062461):0.157442,A_aeolicus-O67117:0.366959):0.172286):0.132253,((S_pombe-Q9USS0:0.569790,((S_c erevisiae-YGD7_YEAST:0.631185,P_falciparum-PFC0910w:0.984402):0.130570,B_burgdorferi-O50718:0.502234 ):0.117639):0.199640,(((N_crassa-NCU00713.1:0.598211,((C_albicans-CA4308:0.000000,C_albicans-CA4286: 0.000000):0.412870,(X_fastidiosa-Q9PB70:0.087709,X_fastidiosa-Q87BY6:0.092008):0.461466):0.110567):0 .148227,((D_melanogaster-Q9VDU7:0.100309,A_gambiae-SANGP00000015741:0.035408):0.618093,(C_elegans-CA E18030:0.391139,C_elegans-Q9N426:0.335560):0.324190):0.212215):0.075249,(V_cholerae-Q9KLN1:0.326523, (((((((E_coli-Q8XDW3:0.000000,(E_coli-Q8XDW3:0.000000,E_coli-PNCA_ECOLI:0.000000):0.000000):0.005287 ,E_coli-Q8FGX8:0.016093):0.005193,(S_flexneri-Q83L62:0.000000,S_flexneri-AAP16947:0.000000):0.010837 ):0.032130,(S_typhimurium-Q8ZPV8:0.005174,(S_typhi-Q8Z6F1:0.000000,S_enterica-Q8Z6F1:0.000000):0.000 000):0.140321):0.175131,(Y_pestis-Q8ZEK5:0.000000,Y_pestis-Q8ZEK5:0.000000):0.220298):0.222467,(A_tu mefaciens-Q8UDQ5:0.000000,A_tumefaciens-Q8UDQ5:0.000000):0.381531):0.147977,((((R_solanacearum-Q8XYJ 8:0.201019,B_japonicum-Q89LJ5:0.281959):0.067344,B_japonicum-Q9REF0:0.260059):0.096862,P_syringae-Q8 7ZX7:0.286372):0.134895,(((B_suis-Q8FZL6:0.015887,B_melitensis-Q8YI99:0.000000):0.229347,R_loti-Q98D 32:0.118603):0.031752,R_meliloti-Q9KHW0:0.120014):0.172005):0.142198):0.043624):0.099919):0.082855): 0.061596):0.166809,C_albicans-CA4287:1.150405):0.732268,(V_vulnificus-Q8DA36:0.288026,V_parahaemolyt icus-Q87JE6:0.205533):0.347826):0.083398,(N_meningitidis-Q9JWU0:0.038732,N_meningitidis-Q9JX97:0.010 684):0.451716):0.118565,P_aeruginosa-Q9HUP5:0.178063):0.349743,L_innocua-Q927S2:0.022535,L_monocytog enes-Q8Y484:0.000000);
PTE2B (tree_in_pdf)	(((((((((((((((((R_norvergicus-IPI00195986.1:0.000000,R_norvergicus-IPI00326667.1:0.000000):0.021162 ,((M_musculus-IPI00130369.1:0.202953,R_norvergicus-IPI00208561.1:0.057268):0.043399,(H_sapiens-IPI00 220906.1:0.017772,H_sapiens-IPI00333838.1:0.000000):0.068917):0.019450):0.013840,H_sapiens-IPI000927 34.2:0.000000):0.000000,(M_musculus-IPI00136683.1:0.000000,M_musculus-IPI00115871.1:0.000000):0.0000 00):0.029079,M_musculus-IPI00281689.1:0.077972):0.086155,R_norvergicus-IPI00210738.1:0.026610):0.016 715,M_musculus-IPI00136676.1:0.046717):0.058529,(M_musculus-IPI00227116.1:0.217496,(R_norvergicus-IP I00210764.1:0.263842,(((M_musculus-IPI00136680.1:0.000000,M_musculus-IPI00308769.1:0.000000):0.04469 9,R_norvergicus-IPI00209803.1:0.009722):0.094248,H_sapiens-IPI00171211.1:0.109366):0.000000):0.13298 4):0.061056):0.058363,((D_rerio-ENSDARP00000011114:0.059253,D_rerio-ENSDARP00000013805:0.104089):0.1 76549,F_rubripens-SINFRUP00000068302:0.270695):0.131073):0.038473,(M_musculus-IPI00270160.1:0.000000 ,H_sapiens-IPI00254180.1:0.544896):0.115804):0.083670,(((R_norvergicus-IPI00194904.1:0.063173,H_sapi ens-IPI00249658.1:0.068959):0.042926,M_musculus-IPI00221606.1:0.000000):0.077899,((M_musculus-IPI003 14202.1:0.025300,R_norvergicus-IPI00207010.1:0.031942):0.265610,H_sapiens-IPI00017819.1:0.115685):0. 121689):0.108885):0.094777,(((C_elegans-O01862:0.539024,C_elegans-O62086:0.107730):0.108547,C_elegan s-O45003:0.148047):0.303508,C_elegans-Q9GYN3:0.315220):0.447769):0.100567,(((F_rubripens-SINFRUP0000 0080315:0.571305,D_rerio-ENSDARP00000007470:0.798452):0.270186,F_rubripens-SINFRUP00000079534:0.3690 56):0.170697,F_rubripens-SINFRUP00000062424:0.269883):0.221766):0.130905,S_mutans-Q8DST1:1.253504):0 .005162,(S_mutans-Q8DV73:0.572367,(C_acetobutylicum-Q97DR5:0.300297,(R_solanacearum-Q8XY76:0.622667, C_crescentus-Q9A9T0:0.480260):0.281745):0.228530):0.173632):0.541346,R_loti-Q98E69:0.292068):0.25214 8,A_tumefaciens-Q8U9S3:0.000000,A_tumefaciens-Q8U9S3:0.000000);
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TES1 (tree_in_pdf)	(((((((((((((((((E_coli-TESB_ECOLI:0.000000,E_coli-TESB_ECOLI:0.000000):0.000000,(E_coli-TESB_ECOLI: 0.000000,(S_flexneri-AAP15930:0.000000,S_flexneri-Q83SF2:0.000000):0.000000):0.000000):0.000000,E_co li-Q8FK97:0.000000):0.000000,(S_typhimurium-Q8ZRB2:0.000000,(S_typhi-Q8Z8U3:0.000000,S_enterica-Q8Z8 U3:0.000000):0.007747):0.077727):0.233318,(Y_pestis-Q8D151:0.000000,Y_pestis-Q8ZC81:0.000000):0.0896 84):0.216601,A_gambiae-SANGP00000000681:0.189202):0.074868,((((V_parahaemolyticus-Q87R49:0.027008,V_ vulnificus-Q8D838:0.017262):0.020009,V_cholerae-Q9KT42:0.091933):0.235055,(H_influenzae-TESB_HAEIN:0 .242464,P_multocida-Q9CN69:0.134009):0.544708):0.125838,S_oneidensis-Q8EFQ7:0.275171):0.109297):0.09 1608,((X_axonopodis-Q8PN30:0.012446,X_campestris-Q8PBH6:0.029320):0.141775,(X_fastidiosa-Q9PEK7:0.00 0000,X_fastidiosa-Q87EJ6:0.007744):0.295752):0.436917):0.020609,((P_putida-Q88DR1:0.117701,P_syringa e-Q87W94:0.123780):0.066035,P_aeruginosa-Q9HX74:0.112355):0.415410):0.057309,A_thaliana-Q9LQ87:1.237 413):0.093407,(((((S_avermitilis-Q82CR2:0.021832,S_coelicolor-Q9L080:0.131741):0.375884,(S_avermitil is-Q82MT5:0.064630,S_coelicolor-Q9KZJ2:0.025514):0.410550):0.136901,((M_bovis-CAD94822:0.000000,(M_t uberculosis-O06209:0.000000,M_tuberculosis-O06209:0.000000):0.000000):0.325189,C_efficiens-Q8FPK1:0. 495833):0.423856):0.119880,C_crescentus-Q9A2B6:0.562927):0.131824,(((R_loti-Q98EG9:0.351324,(B_suis- Q8FYH7:0.000000,B_melitensis-Q8YJC0:0.000000):0.172412):0.054822,((A_tumefaciens-Q8UBU4:0.000000,A_t umefaciens-Q8UBU4:0.000000):0.167070,R_meliloti-Q92L92:0.220676):0.086211):0.160439,B_japonicum-Q89W S4:0.447244):0.114835):0.024508):0.186340,M_leprae-Q9CC48:1.396265):0.084072,(N_crassa-NCU00580.1:0. 884181,(S_cerevisiae-PTE1_YEAST:1.825146,(C_albicans-CA1609:1.700565,C_albicans-CA1608:0.623725):1.0 05152):0.493662):0.372711):0.194895,(((((M_musculus-IPI00227666.1:0.114452,R_norvergicus-IPI00204659 .1:0.531460):0.147999,M_musculus-IPI00309365.1:0.000000):0.034463,R_norvergicus-IPI00207110.1:0.0230 03):0.025584,H_sapiens-IPI00298202.1:0.094218):0.176123,F_rubripens-SINFRUP00000084567:0.200490):0.3 52565):0.456651,(C_elegans-Q19781:0.142426,C_elegans-Q95Q68:0.407680):0.350303):0.438162,(C_elegans- Q9BIA9:0.000000,C_elegans-Q9BIA5:0.000000):0.430255):0.701506,C_elegans-Q18061:0.369712,C_elegans-AA K31417:0.000000);
URIC (tree_in_pdf)	(((((S_coelicolor-Q8CJN8:0.225085,S_avermitilis-Q82LJ2:0.120601):0.621395,D_radiodurans-Q9RV70:0.965 134):0.152173,(((A_gambiae-SANGP00000019313:0.274237,D_melanogaster-URIC_DROME:0.217356):0.388530,(( (M_musculus-IPI00223367.2:0.040696,R_norvergicus-IPI00231365.2:0.016930):0.015325,H_sapiens-IPI00258 342.1:0.378526):0.108159,(F_rubripens-SINFRUP00000063883:0.086597,F_rubripens-SINFRUP00000063882:0.0 08073):0.371511):0.411059):0.351900,A_thaliana-URIC_ARATH:0.830302):0.099738):0.186586,((S_pombe-URI C_SCHPO:0.508651,C_albicans-CA2731:0.727864):0.161807,N_crassa-NCU07853.1:0.438286):0.199085):1.4647 33,B_halodurans-Q9KEU0:0.460009,B_subtilis-URIC_BACSU:0.431374);
YGR154C (tree_in_pdf)	((((((((((((((((S_flexneri-Q83JI7:0.000000,S_flexneri-AAP18429:0.000000):0.000000,E_coli-YQJG_ECOLI: 0.011530):0.005782,(E_coli-Q8XAH0:0.000000,E_coli-Q8XAH0:0.000000):0.000000):0.010132,(S_typhimurium -Q8ZLW8:0.011564,(S_typhi-Q8Z3L1:0.000000,S_enterica-Q8Z3L1:0.000000):0.000000):0.060304):0.129099,Y _pestis-Q8D1R8:0.156885):0.144441,(S_agalactiae-Q8E0D4:0.000000,S_agalactiae-Q8E608:0.000000):0.5016 54):0.030531,((X_campestris-Q8P4Y7:0.114279,X_axonopodis-Q8PPV0:0.057437):0.148788,Synechocystis_sp. -P74752:0.169159):0.132178):0.042288,(((B_suis-Q8FZC9:0.011309,B_melitensis-Q8YII9:0.011215):0.21182 0,R_loti-Q98HM6:0.194154):0.094767,((P_aeruginosa-Q9I0M8:0.154214,(P_putida-Q88FT4:0.188560,P_syring ae-Q87ZT1:0.137195):0.042712):0.137684,(N_europaea-Q82WY2:0.497345,((V_parahaemolyticus-Q87MZ0:0.123 747,V_vulnificus-Q8D8A4:0.102518):0.133280,V_cholerae-Q9KT09:0.060959):0.246953):0.119089):0.073359) :0.068206):0.064698,(R_meliloti-Q92N54:0.176869,(A_tumefaciens-Q8UD66:0.000000,A_tumefaciens-Q8UD66: 0.000000):0.223300):0.169333):0.114511,((((S_cerevisiae-YM85_YEAST:0.319642,S_cerevisiae-YK56_YEAST: 0.155623):0.104714,S_cerevisiae-YG3P_YEAST:0.822961):0.195163,C_albicans-CA2386:0.211563):0.267469,( N_crassa-NCU04368.1:0.289192,(S_pombe-O94524:0.342767,N_crassa-NCU09570.1:0.884717):0.059992):0.0241 22):0.371110):0.035425,((A_thaliana-O81869:0.095778,A_thaliana-Q9FL95:0.137135):0.022085,A_thaliana- Q9FL98:0.201669):0.564555):0.112858,(Halobacterium_sp.-Q9HN26:0.434645,((S_coelicolor-O85700:0.07477 8,S_avermitilis-Q825J4:0.044016):0.268272,(C_glutamicum-Q8NR03:0.074257,C_efficiens-Q8FPX9:0.027816) :0.416212):0.374894):0.051757):0.338942,A_thaliana-Q9FNC6:0.606514):0.051228,Anabaena_sp.-Q8YPZ4:0.2 88406):0.146162,P_marinus-AAP99296:1.237555):2.079941,S_agalactiae-Q8E4L0:0.000000,S_agalactiae-Q8DZ 01:0.005528);