#NEXUS [written Wed Apr 02 17:04:29 BST 2014 by Mesquite version 2.75 (build 564) at BIO-FBH98W1-TSG/144.173.145.112] BEGIN TAXA; TITLE 'Species_list_nuclear_receptors'; DIMENSIONS NTAX=131; TAXLABELS Homo_sapiens_THRa Homo_sapiens_THRb Crassostrea_gigas_NR1A Crassostrea_gigas_NR1B Homo_sapiens_RARa Homo_sapiens_RARb Homo_sapiens_RARg Lymnaea_stagnalis_RAR Homo_sapiens_PPARa Homo_sapiens_PPARb Homo_sapiens_PPARg Crassostrea_gigas_NR1C Homo_sapiens_Reverba Homo_sapiens_Reverbb Mytilus_galloprovincialis_NR1Dv1 Crassostrea_gigas_NR1D Caenorhabditis_elegans_NHR85 Drosophila_melanogaster_E75 Crassostrea_gigas_NR1CDEFa Crassostrea_gigas_NR1CDEFb Mytilus_galloprovincialis_NR1DEF Crassostrea_gigas_NR1E Drosophila_melanogaster_E78 Caenorhabditis_elegans_SEX1 Homo_sapiens_RORa Homo_sapiens_RORb Homo_sapiens_RORg Crassostrea_gigas_NR1F Caenorhabditis_elegans_NHR23 Drosophila_melanogaster_DHR3 Homo_sapiens_LXRb Homo_sapiens_LXRa Crassostrea_gigas_NR1H Drosophila_melanogaster_EcR Homo_sapiens_FXR Homo_sapiens_VDR Homo_sapiens_PXR Homo_sapiens_CAR Drosophila_melanogaster_DHR96 Caenorhabditis_elegans_DAF12 Caenorhabditis_elegans_NHR8 Crassostrea_gigas_NR1Ja Crassostrea_gigas_NR1Jb Crassostrea_gigas_NR1Jg Crassostrea_gigas_NR2A Caenorhabditis_elegans_NHR64 Caenorhabditis_elegans_NHR69 Homo_sapiens_HNF4a Homo_sapiens_HNF4b Drosophila_melanogaster_HNF4 Crassostrea_gigas_NR2B Homo_sapiens_RXRa Homo_sapiens_RXRb Homo_sapiens_RXRg Lymnaea_stagnalis_RXR Biomphalaria_glabrata_RXR Thais_clavigera_RXR Nucella_lapillus_RXR Drosophila_melanogaster_USP Crassostrea_gigas_NR2CD Caenorhabditis_elegans_NHR41 Homo_sapiens_TR2 Homo_sapiens_TR4 Drosophila_melanogaster_DHR78 Homo_sapiens_TLX Drosophila_melanogaster_DSF Crassostrea_gigas_NR2E5 Crassostrea_gigas_NR2E1 Crassostrea_gigas_NR2E2 Drosophila_melanogaster_TLL Drosophila_melanogaster_DHR51 Crassostrea_gigas_NR2E3 Drosophila_melanogaster_DHR83 Caenorhabditis_elegans_FAX1 Homo_sapiens_PNR Homo_sapiens_COUPTF1 Homo_sapiens_COUPTF2 Homo_sapiens_EAR2 Drosophila_melanogaster_SVP Caenorhabditis_elegans_UNC55 Crassostrea_gigas_NR2F Homo_sapiens_ERa Homo_sapiens_ERb Mytilus_edulis_ER Crassostrea_gigas_ER Octopus_vulgaris_ER Aplysia_californica_ER Thais_clavigera_ER Marisa_cornuarietis_ER Nucella_lapillus_ER Crassostrea_gigas_NR3A Homo_sapiens_ERRa Homo_sapiens_ERRb Homo_sapiens_ERRg Marisa_cornuarietis_ERR Crassostrea_gigas_NR3B Drosophila_melanogaster_DERR Homo_sapiens_GR Homo_sapiens_MR Homo_sapiens_PR Homo_sapiens_AR Crassostrea_gigas_NR4A Drosophila_melanogaster_DHR38 Caenorhabditis_elegans_NHR6 Homo_sapiens_NGFIB Homo_sapiens_NURR1 Homo_sapiens_NOR1 Homo_sapiens_SF1 Homo_sapiens_LRH Crassostrea_gigas_NR5B Caenorhabditis_elegans_NHR25 Drosophila_melanogaster_FTZF1 Drosophila_melanogaster_DHR39 Crassostrea_gigas_NR5A Caenorhabditis_elegans_NHR91 Drosophila_melanogaster_DHR4 Homo_sapiens_GCNF Crassostrea_gigas_NHR43 Crassostrea_gigas_NR1P7 Crassostrea_gigas_NR1P1 Crassostrea_gigas_NR1P3 Crassostrea_gigas_NR1P8 Crassostrea_gigas_NR1P9 Crassostrea_gigas_NR1P6 Crassostrea_gigas_NR1P4 Crassostrea_gigas_NR1P5 Crassostrea_gigas_NR1P2 Crassostrea_gigas_NR1P10 Mytilus_galloprovincialis_NR1G Crassostrea_gigas_NR1P11 Crassostrea_gigas_NHR42 ; END; BEGIN CHARACTERS; TITLE 'nuclear_receptor_aa_sequences_matrix'; DIMENSIONS NCHAR=221; FORMAT DATATYPE = Protein GAP = - MISSING = ?; MATRIX Homo_sapiens_THRa CVVCGDKATGYHYRCITCEGCKGFFRRTI----QKNLHPTYS-CKY-DS----CCVIDKITRNQ---CQLCRFKKCIAVGMAMDFSEFTKIITPAITRVVDFAKKLPMFSELPCEDQIILLKGCCMEIMSLRAAVRYDPESVSDAIF---ELGKSLSA-FNLDDTEVALLQAVLLMSGLLCVDKIEKSQEAYLLAFEHYVNHRKHFWPKLLMKVTDLRMIG Homo_sapiens_THRb CVVCGDKATGYHYRCITCEGCKGFFRRTI----QKNLHPSYS-CKY-EG----KCVIDKVTRNQ---CQECRFKKCIYVGMATDFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESVSDAIF---DLGMSLSS-FNLDDTEVALLQAVLLMSGLACVERIEKYQDSFLLAFEHYINYRKHFWPKLLMKVTDLRMIG Crassostrea_gigas_NR1A CVVCGDAATGYHYRCMTCEGCKGFFRRTI----QKNL--QYH-CKW-NK----MCSIDKNSRNQ---CQECRFRKCLNVGMATDWQQLAEAMTPSIVKVVEFAKNVPGFIQLFVDDQILLLKSCCMEIMCLRAACRYDPEKLVEPIF---EFAVGLSK-LKLDKTELALLAAVLLMQGLKEPEAVEKLQDSILGAFKRYIATKRVHWAKILMKVTDLRTIS Crassostrea_gigas_NR1B CVVCSDKSSGYHYGVSSCEGCKGFFRRSV----QKNM--QYT-CHK-DK----NCPINKVTRNR---CQYCRLQKCYATGMSKEWDKVTELSSKGIIKIVEFAKKMPGFTSLSTSDQITLLKAACLEIMILRLCSRYDLDKLTDTIF---RFASSLKV-LNIDEMEYAVLSAICLISGLEESERVEQMQEPILEALKHYVRTRRNVFAKILYKLTDLRSIS Homo_sapiens_RARa CFVCQDKSSGYHYGVSACEGCKGFFRRSI----QKNM--VYT-CHR-DK----NCIINKVTRNR---CQYCRLQKCFEVGMSKEWDKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQLTDLVF---AFANQLLP-LEMDDAETGLLSAICLICDLEQPDRVDMLQEPLLEALKVYVRKRRHMFPKMLMKITDLRSIS Homo_sapiens_RARb CFVCQDKSSGYHYGVSACEGCKGFFRRSI----QKNM--IYT-CHR-DK----NCVINKVTRNR---CQYCRLQKCFEVGMSKEWDKFSELATKCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDILILRICTRYTPEQLTDLVF---TFANQLLP-LEMDDTETGLLSAICLICDLEEPTKVDKLQEPLLEALKIYIRKRRHMFPKILMKITDLRSIS Homo_sapiens_RARg CFVCNDKSSGYHYGVSSCEGCKGFFRRSI----QKNM--VYT-CHR-DK----NCIINKVTRNR---CQYCRLQKCFEVGMSKEWDKFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQLTDLVF---AFAGQLLP-LEMDDTETGLLSAICLICDLEEPEKVDKLQEPLLEALRLYARRRRYMFPRMLMKITDLRGIS Lymnaea_stagnalis_RAR CVVCNDKSSGYHYGVSSCEGCKGFFRRSV----QKNM--QYT-CHK-EK----NCVINKVTRNR---CQYCRLQKCVVMGMSKEWEKITELSSAGIVMIVDFAKKIPGFLSLSTSDQITLLKAACLEIMILRISIRYELDTLTSTIF---SFAASLKR-MNCDETEYAMLSSICLISGLHDTEKIEQMQEPLLEALKHYIRSRRHTFAKMLMKLTDLRSIS Homo_sapiens_PPARa CRICGDKASGYHYGVHACEGCKGFFRRTI----RLKL--VYDKC---DR----SCKIQKKNRNK---CQYCRFHKCLSVGMSHNFHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGIMEPKF---DFAMKFNA-LELDDSDISLFVAAIICCGLLNVGHIEKMQEGIVHVLRLHLQSNHFLFPKLLQKMADLRQLV Homo_sapiens_PPARb CRVCGDKASGFHYGVHACEGCKGFFRRTI----RMKL--EYEKC---ER----SCKIQKKNRNK---CQYCRFQKCLALGMSHNFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNKDGIIEPKF---EFAVKFNA-LELDDSDLALFIAAIILCGLMNVPRVEAIQDTILRALEFHLQANHYLFPKLLQKMADLRQLV Homo_sapiens_PPARg CRVCGDKASGFHYGVHACEGCKGFFRRTI----RLKL--IYDRC---DL----NCRIHKKSRNK---CQYCRFQKCLAVGMSHNFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGFMEPKF---EFAVKFNA-LELDDSDLAIFIAVIILSGLLNVKPIEDIQDNLLQALELQLKLNHQLFAKLLQKMTDLRQIV Crassostrea_gigas_NR1C CKICGDKASGFHYGVFSCEGCKGFFRRTV----RQKL--VYKPCEN-PK----GCLIMRISRNR---CQYCRMQRCIMAGMSHERKFCSQYVTDMVRFISIFAREIPQFTQMDIDDQKTLIKHCILESIIIHCVSRSPSDCLIYDVV---TCVKKLKA-LRLTEVELAIFAAMVLFCDLKCSDVLEKMEIELYLALKCQFLLNHNLFPKIVEIICSIRAIT Homo_sapiens_Reverba CKVCGDVASGFHYGVHACEGCKGFFRRSI----QQNI--QYKRCLK-NE----NCSIVRINRNR---CQQCRFKKCLSVGMSRDWEDFSMSFTPAVREVVEFAKHIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFNVKDLLSAMF---DFSEKLNS-LALTEEELGLFTAVVLVSGMENSASVEQLQETLLRALRALVLKNRSRFTKLLLKLPDLRTLN Homo_sapiens_Reverbb CKVCGDVASGFHYGVHACEGCKGFFRRSI----QQNI--QYKKCLK-NE----NCSIMRMNRNR---CQQCRFKKCLSVGMSRDWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLFDAKELLNSMF---EFSEKLNA-LQLSDEEMSLFTAVVLVSGIENVNSVEALQETLIRALRTLIMKNHSIFTKLLLKLPDLRSLN Mytilus_galloprovincialis_NR1Dv1 CRVCGDKASGFHYGVHACEGCKGFFRRSI----QQKI--QYRPCLK-NQ----QCNIMRVNRNR---CQYCRLKKCIAVGMSRDWEDFYDFYTPAIISVVNFAKSVPGFCILNQDDQVTLLKAATFEVLLVRHACLFDTDNLLDSMF---DFAERFNM-LKLAEEEIALFSAIVLLSGLRNVEQIEKLQNKLTESLQTVINTNHTLFAKLLMKTTNLRTLN Crassostrea_gigas_NR1D CRVCGDKASGFHYGVHACEGCKGFFRRSI----QQKI--QYRPCLK-NQ----QCNIMRVNRNR---CQYCRLKKCIAVGMSRDWSDMSEFFTPAIKSVVDFAKAIPGFCFLSQDDQVTLLKAATFEVLLVRMACLFDPESLLDSMF---DFADRFNK-LNLTDEEVAIFSAIVLLSGLRNVEQLESFQMKLTECLQSMITANHTLFAKLLMKTTDLRTLN Caenorhabditis_elegans_NHR85 CQVCSDKASGFHYGVFACEGCKGFFRRSI----QQKI--TYRACTR-AE----DCLILRNNRNR---CQCCRLKKCLAVGMSRDCPITSNFIVIPLKAAIDFANSIPAFLSITQTQRVHLLQNSVFDVMLLASASASTSQHIPQAIQ---SISARIRQ---LPPQTVPILTAIAVCQLLPESQQPMLLAERLWCVLGKLGGIQSATAPSLLADVRTLRQWH Drosophila_melanogaster_E75 CRVCGDKASGFHYGVHSCEGCKGFFRRSI----QQKI--QYRPCTK-NQ----QCSILRINRNR---CQYCRLKKCIAVGMSRDEQEFSQRFAHVIRGVIDFAGMIPGFQLLTQDDKFTLLKAGLFDALFVRLICMFDSSILVDSTF---NFAERMNS-MNLTDAEIGLFCAIVLITGLRNLELIEKMYSRLKGCLQYIVAQNREFLAKLLETMPDLRTLS Crassostrea_gigas_NR1CDEFa CKVCGDESSGFHYGVDSCEGCKGFFRRCI----TQGM--THK-CSN-EE----KCEITPFTRNS---CQYCRLKKCFAVGMSREWQQFVSQMVPEITLVVKFCKKIPGFGEIDQEDQINLIKQGSFEVMLCRFCNLVDYKKFMDEFF---NVAEMFNP-LKLTDGEIGLFTSTLIICDYDNVFMKAVSTMRTFKVVNLKHRIALDMFPPLHCEVFEHGDCS Crassostrea_gigas_NR1CDEFb CLVCGDRSSGIHYGVLACEGCKGFFRRAL----QDIGDPARKRCYY-NK----SCDITILTRNR---CQYCRLQKCLALGMSRSWEGFQSLLNKTIQDTVIFAKKIPGFPHLDQDDQISLIKGGCFEVACVIHSKFIDSDTFVELFF---NLCVRFNA-YKLGDAEKALFSALVLISGLKNREKVSKLQELLIQALQTQITQSHGLFPRLLMSISSLRELG Mytilus_galloprovincialis_NR1DEF -----------------CEGCKGFFRRCI----TQGM--THK-CSN-EE----KCEITPFTRNS---CQYCRLKKCFAVGMSREWEQFVQNMVPEITMVVKFCKKIPGFNEICQEDQINLIKQGSFEVMLVRMCNLVDTEKFLVEFF---KVAKAFNP-LQLTDGEIGIFTATLIICSIINSVAIMKLQLLLMQALYVLIKKNHSLFIELMKRIPIFRGIN Crassostrea_gigas_NR1E CKVCGDRASGFHYGVTSCEGCKGFFRRSI----QKQI--EYR-CLR-DG----KCMVIRLSRNR---CQYCRFKKCLAVGMSRDWHCLASFITPAINSVVEFAKRVTGFPELNQDDQLILIKCGFFEVWLMRMARMFNKAEFVSCMF---DLAQSLNQ-LNLNDTEIGLFCAIVLATGLENPKAVETIQDRLIEALKLQILRNHNLFGTTIVKLPQLRTLG Drosophila_melanogaster_E78 CKVCGDKASGYHYGVTSCEGCKGFFRRSI----QKQI--EYR-CLR-DG----KCLVIRLNRNR---CQYCRFKKCLSAGMSRDWQQFSARVTPGVQRIVEFAKRVPGFCDFTQDDQLILIKLGFFEVWLTHVARLINEATFVNALL---NFANTLNA-YGLSDTEIGLFSAMVLLAGLSEPKVIGRARELVAEALRVQILRSRQLMPALEAKIPELRSLG Caenorhabditis_elegans_SEX1 CKVCGDKASGYHYGVTSCEGCKGFFRRSI----QRKI--DYR-CLK-QQ----VCEIKRESRNR---CQYCRFKKCLDSGMSKDWQIYAHEIDVDIKEVVNFVKEIPKFNFINGNDKAVLLRKNAFPLYLLRIVRGMSNRGLADEML---AFANHIIT-IGCTDGDIALFIVLILCQNFKSQLQLLEMFDFYKKVLFQKMTCRIDTYKQLMKCIHELNRLN Homo_sapiens_RORa CKICGDKSSGIHYGVITCEGCKGFFRRSQ----QSNA--TYS-CPR-QK----NCLIDRTSRNR---CQHCRLQKCLAVGMSRDWQLCAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQNFISFVF---EFGKSLCS-MHLTEDEIALFSAFVLMSWLQEKVKIEKLQQKIQLALQHVLQKNHGILTKLICKVSTLRALC Homo_sapiens_RORb CKICGDKSSGIHYGVITCEGCKGFFRRSQ----QNNA--SYS-CPR-QR----NCLIDRTNRNR---CQHCRLQKCLALGMSRDWQQCAIQITHAIQYVVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLNLVNEAF---DFAKNLCS-LQLTEEEIALFSSAVLISWLIEPRKVQKLQEKIYFALQHVIQKNHETLAKLIAKIPTITAVC Homo_sapiens_RORg CKICGDKSSGIHYGVITCEGCKGFFRRSQ----RCNA--AYS-CTR-QQ----NCPIDRTSRNR---CQHCRLQKCLALGMSRDWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNLISSIF---DFSHSLSA-LHFSEDEIALYTALVLINGLQEKRKVEQLQYNLELAFHHHLCKTH--RQSILAKLPPLRSLC Crassostrea_gigas_NR1F CKVCGDKSSGVHYGIITCEGCKGFFRRSQ----AGPV--NYQ-CPR-NK----NCVIDRVNRNR---CQFCRLQKCLALGMSRDWSEVAEKITIAVQQIIEFAKMLPGFMDLSQDDQIMLLKAGSFELALIRACRVFDERTLREQVF---EFVRNVIQ-LKLTESQLALFSAVVLIRGLKDIADVQKLNEKVLTALKQELGKTHNVLTRLMQLTWTLRQLS Caenorhabditis_elegans_NHR23 CKVCGDKSSGVHYGVITCEGCKGFFRRSQ----SSIV--NYQ-CPR-QK----NCVVDRVNRNR---CQYCRLKKCIELGMSRDWELFARELNPLIQAIIEFAKSIDGFMNLPQETQIQLLKGSVFELSLVFAAMYYNVDALIVEVN---NTLQEIVH-LQPHQSELALLAAGLILEGILDTATIAT-AETLKNALYQSVMPRIDTIHRIQDVETRIRQTA Drosophila_melanogaster_DHR3 CKVCGDKSSGVHYGVITCEGCKGFFRRSQ----SSVV--NYQ-CPR-NK----QCVVDRVNRNR---CQYCRLQKCLKLGMSRDWLDCAEKLTQMIQNIIEFAKLIPGFMRLSQDDQILLLKTGSFELAIVRMSRLLDLSQLVSRIF---QTAKSIAE-LKLTETELALYQSLVLLWGVRGNTEIQRLFNLSMNAIRQELETNHTVLDTLLNNIPNFRDIS Homo_sapiens_LXRb CRVCGDKASGFHYNVLSCEGCKGFFRRSV----VRGGARRYA-CRG-GG----TCQMDAFMRRK---CQQCRLRKCKEAGMREQFAHFTELAIISVQEIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETARRYNHETFINPIF---EFSRAMRR-LGLDDAEYALLIAINIFSNVQEPGRVEALQQPYVEALLSYTRIKRLRFPRMLMKLVSLRTLS Homo_sapiens_LXRa CSVCGDKASGFHYNVLSCEGCKGFFRRSV----IKGA--HYI-CHS-GG----HCPMDTYMRRK---CQECRLRKCRQAGMREEFAHFTELAIVSVQEIVDFAKQLPGFLQLSREDQIALLKTSAIEVMLLETSRRYNPGSFINPIF---EFSRAMNE-LQLNDAEFALLIAISIFSNVQDQLQVERLQHTYVEALHAYVSIHHLMFPRMLMKLVSLRTLS Crassostrea_gigas_NR1H CRICGDRASGYHYNALSCEGCKGFFRRSI----TRGA--SYN-CKY-GG----NCEMDMWMRRK---CQSCRLKRCREVGMKEELSSLSKMTVLITHLIVEYAKSLPGFSKLNKEDQIILLKAASSEVMALRASRMYDPASYTELVF---KLCHDMAD-LNSDNAEYALFTAISIFSGLTNRDLVEQIQKVYVDALEEYENKKRCGLAKYLLRLIDLRNIS Drosophila_melanogaster_EcR CLVCGDRASGYHYNALTCEGCKGFFRRSV----TKSA--VYC-CKF-GR----ACEMDMYMRRK---CQECRLKKCLAVGMRPEFRHITEITILTVQLIVEFAKGLPAFTKIPQEDQITLLKACSSEVMMLRMARRYDHSSNIEDLL---HFCRQMFS-MKVDNVEYALLTAIVIFSGLEKAQLVEAIQSYYIDTLRIYILNRHVFYAKLLSILTELRTLG Homo_sapiens_FXR CVVCGDRASGYHYNALTCEGCKGFFRRSI----TKNA--VYK-CKN-GG----NCVMDMYMRRK---CQECRLRKCKEMGMLAEFLILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLYITPMF---SFYKSIGE-LKMTQEEYALLTAIVILSYIKDREAVEKLQEPLLDVLQKLCKIHQQHFACLLGRLTELRTFN Homo_sapiens_VDR CGVCGDRATGFHFNAMTCEGCKGFFRRSM----KRKA--LFT-CPF-NG----DCRITKDNRRH---CQACRLKRCVDIGMMKELPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDLIEPLI---KFQVGLKK-LNLHEEEHVLLMAICIVSGVQDAALIEAIQDRLSNTLQTYIRCRHLLYAKMIQKLADLRSLN Homo_sapiens_PXR CRVCGDKATGYHFNVMTCEGCKGFFRRAM----KRNA--RLR-CPFRKG----ACEITRKTRRQ---CQACRLRKCLESGMKKELPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETLLEPML---KFHYMLKK-LQLHEEEYVLMQAISLFSGVLQHRVVDQLQEQFAITLKSYIECNRFLFLKIMAMLTELRSIN Homo_sapiens_CAR CVVCGDQATGYHFNALTCEGCKGFFRRTV----SKSI--GPT-CPF-AG----SCEVSKTQRRH---CPACRLQKCLDAGMRKDVTHFADINTFMVLQVIKFTKDLPVFRSLPIEDQISLLKGAAVEICHIVLNTTFCLQTFLELLF---HFHGTLRK-LQLQEPEYVLLAAMALFSGVTQRDEIDQLQEEMALTLQSYIKGQQFLYAKLLGLLAELRSIN Drosophila_melanogaster_DHR96 CAVCGDKALGYNFNAVTCESCKAFFRRNA----LAKK--QFT-CPF-NQ----NCDITVVTRRF---CQKCRLRKCLDIGMKSELLQLINLTAVAIKRLIKMAKKITAFRDMCQEDQVALLKGGCTEMMIMRSVMIYDDDRIYEEHQ---KFITTFDEKWRMDENIILIMCAIVLFTRVIHKDVIRLEQNSYYYLLRRYLESVYNAFIKLIQKISDVERLN Caenorhabditis_elegans_DAF12 CRVCGDHATGYNFNVITCESCKAFFRRNA----LRPK--EFK-CPY-SE----DCEINSVSRRF---CQKCRLRKCFTVGMKKEPADIMNIMDVTMRRFVKVAKGVPAFREVSQEGKFSLLKGGMIEMLTVRGVTRYDASTQKAKCL---EFFGFFDEEIKKNELAVYLVMLAVLFSNENDVRIVTERHNHFMSLLNRYLESLFRIFERIPKALGLLNEIA Caenorhabditis_elegans_NHR8 CTVCSDRANGYNFGVLTCESCKAFFRRNA----SKHK--EIK-CPF-SD----SCQITSASRKF---CQACRLNKCFAVGMNSEIDGVFRIIEEALRRIVNMACQLSLFRELHVDDRKNLLKSGFGELLIVRGLMAYDKSDHYKAHM---NLLSTFGEDVRNNEHLMLIFNAAVIFHNLRDSKRVHSTQAKYFQMLLKLLTFEYIAYSNLLNQVVELHRVN Crassostrea_gigas_NR1Ja CGVCGDKALGYNFDAITCESCKAFFRRNA----LKTK--VFA-CSF-DG----NCKLDTHTRKF---CSGCRLKKCFDIGMKKEANDLFNLTDIFIRRLIKFAKHVPEFKQLQQEDQIHLLKGGIMEIMVLRSVMGFDAQAMYSDHV---KFVMSLNQLTKANKTILTLLFVIELFSSLKNKELVAKGQEKFSTWLQAYLESIYQLYPKLLMKLLDVRSLG Crassostrea_gigas_NR1Jb CGVCGDRALGYNFDAISCESCKAFFRRNA----PKGL--EYFKCPY-EE----KCKMDVSNRRF---CKRCRLRKCFEIGMRKEMKDLVNIAELSVRRVIDMAKKIKSFKALSQTDQISLLKGGSIELLILRSVISFDKEKLFAEHM---KFTKSLAVDLKADETMLILLLVISLFSNISDKSYVCQEQEKYALLLLRYLESRYAIYPKLLMKLTDIRDLN Crassostrea_gigas_NR1Jg CLVCGDKALGYNFNAVSCESCKAFFRRNA----HKVI--RGR-C---EG----RCDITVESRSF---CKKCRLAKCFTVGMRKDATEFVNLAEGFVRRIIKVAKNIEFFKMICKEDQIALLKGSVVEIMMLRSAINYNVETMFLTYS---KFIKSLMRTIHGDLLALKLLIMLSLFSGVLEHDKIQQIQECYAGILQKYVERRFIMFAKIVMKLTDLRNIN Crassostrea_gigas_NR2A CAICGDRATGKHYGASSCDGCKGFFRRSV----RKNH--VYS-CRF-NR----NCVVDKDKRNQ---CRYCRLRKCFRAGMKKEANDVCESMKQQLLILVEWAKYIPCFCELTIDDQVALLRAHAGEHLIMGVARRSLGVKVASRIL--DELVQPMKD-VQMDESEFACLKAIVFFDGLTDPQKIKSFRYQVQVNLEDYINDRQGRFGEILLMLPPLQSIT Caenorhabditis_elegans_NHR64 CAICGDRATGKHYGAMSCDGCKGFFRRTI----RKRH--SYV-CRF-GE----KCQVDKAKRNS---CRKCRFDVCLRKGMRRDTNDVTDSMNQQLTLMVEWAKVLEGFQRVDNITQVALLRHFSAQHLVMCAAFRSIHLSVAERII--DQVTNPMRS-LHMNEIEYIALKAIAFFDGIESYSDVEEMRQRILESFERHVRYVSLRFANLLLLLPPMLAIS Caenorhabditis_elegans_NHR69 CHICNDKSTGKHYGAISCDGCKGFFRRSI----RKRY--HYQ-CRF-EQ----NCDVTKNKRNA---CRACRLQKCVKAGMKSNLDDIGKSIHQQLVLFIEWAKSLPQFSFLAQADQAALLKGGAASIIVLGVAYRSICLTVVGRII--DEIVNPMRR-LNMDLIEYVALKAILFFNEINDQSPVENARYAFLRSLQRRCTDKACRSGKLLLLLPSLQAIA Homo_sapiens_HNF4a CAICGDRATGKHYGASSCDGCKGFFRRSV----RKNH--MYS-CRF-SR----QCVVDKDKRNQ---CRYCRLKKCFRAGMKKEIADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKVSIRIL--DELVLPFQE-LQIDDNEYAYLKAIIFFDGLSDPGKIKRLRSQVQVSLEDYINDRQGRFGELLLLLPTLQSIT Homo_sapiens_HNF4b CAICGDRATGKHYGASSCDGCKGFFRRSI----RKSH--VYS-CRF-SR----QCVVDKDKRNQ---CRYCRLRKCFRAGMKKEIGDVCESMKQQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMMYKVANRVL--DELVRPFQE-IQIDDNEYACLKAIVFFDGLSDPVKIKNMRFQVQIGLEDYINDRQGRFGELLLLLPTLQSIT Drosophila_melanogaster_HNF4 CAICGDRATGKHYGASSCDGCKGFFRRSV----RKNH--QYT-CRF-AR----NCVVDKDKRNQ---CRYCRLRKCFKAGMKKEINDVCESMKQQLLTLVEWAKQIPAFNELQLDDQVALLRAHAGEHLLLGLSRRSMHLKIGARII--DELVTVMKD-VGIDDTEFACIKALVFFDGLNEPHRIKSLRHQILNNLEDYISDRQGRFGEILLILPVLQSIT Crassostrea_gigas_NR2B CAICGDRASGKHYGVYSCEGCKGFFKRTV----RKDL--TYA-CRD-DR----NCIIDKRQRNR---CQYCRYMKCLNMGMKREVTNICQAADKQLFTLVEWAKRIPHFTELPLEDQVILLRAGWNELLIAGFSHRSIVVKIFDRVL--TELVAKMRE-MKMDKTELGCLRAIVLFNGVSAVSEVEQLREKVYASLEEYCKMHYGRFAKLLLRLPALRSIG Homo_sapiens_RXRa CAICGDRSSGKHYGVYSCEGCKGFFKRTV----RKDL--TYT-CRD-NK----DCLIDKRQRNR---CQYCRYQKCLAMGMKREVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKIFDRVL--TELVSKMRD-MQMDKTELGCLRAIVLFNGLSNPAEVEALREKVYASLEAYCKHKYGRFAKLLLRLPALRSIG Homo_sapiens_RXRb CAICGDRSSGKHYGVYSCEGCKGFFKRTI----RKDL--TYS-CRD-NK----DCTVDKRQRNR---CQYCRYQKCLATGMKREVTNICQAADKQLFTLVEWAKRIPHFSSLPLDDQVILLRAGWNELLIASFSHRSIDVRIFDRVL--TELVSKMRD-MRMDKTELGCLRAIILFNGLSNPSEVEVLREKVYASLETYCKQKYGRFAKLLLRLPALRSIG Homo_sapiens_RXRg CAICGDRSSGKHYGVYSCEGCKGFFKRTI----RKDL--IYT-CRD-NK----DCLIDKRQRNR---CQYCRYQKCLVMGMKREVTNICHAADKQLFTLVEWAKRIPHFSDLTLEDQVILLRAGWNELLIASFSHRSVSVQIFDRVL--TELVSKMKD-MQMDKSELGCLRAIVLFNGLSNPSEVETLREKVYATLEAYTKQKYGRFAKLLLRLPALRSIG Lymnaea_stagnalis_RXR CAICGDRASGKHYGVYSCEGCKGFFKRTV----RKDL--TYA-CRD-DK----NCMIDKRQRNR---CQYCRYMKCLSMGMKREVTNICQAADKQLFTLVEWAKRIPHFTELPLEDQVILLRAGWNELLIAGFSHRSIMAKIFDRVL--TELVAKMRE-MKMDKTELGCLRAVVLFNGLTAVQEVEQLREKVYASLEEYTKTRYGRFAKLLLRLPALRSIG Biomphalaria_glabrata_RXR CAICGDRASGKHYGVYSCEGCKGFFKRTV----RKDL--TYA-CRD-DK----NCMIDKRQRNR---CQYCRYMKCLSMGMKREVTNICQAADKQLFTLVEWAKRIPHFTELPLEDQVILLRAGWNELLIAGFSHRSIMAKIFDRVL--TELVAKMRD-MKMDKTELGCLRAVVLFNGLTAVQEVEQLREKVYASLEEYTKSRYGRFAKLLLRLPALRSIG Thais_clavigera_RXR CAICGDRASGKHYGVYSCEGCKGFFKRTV----RKDL--TYA-CRD-DK----NCMIDKRQRNR---CQYCRYMKCLAQGMKREVTNICQAADKQLFTLVDWAKRIPHFVELPLEDQVILLRAGWNELLIGGFSHRSTQVTIFDRVL--TELVAKMRE-MKMDKTELGCLRAIVLFNGLQSVQEVEQLREKVYASLEEYCKQRYGRFAKLLLRLPALRSIG Nucella_lapillus_RXR CAICGDRASGKHYRVYSCEGCKGFFKRTV----RKDP--TYA-CRD-DK----NCMIDKRQRNR---CQFCRYMKCLAQGMKREVTNICQAADKQLFTLVEWAKRIPHFIELPLEDQVILLRAGWNELLIAGFSHRSTQVTIFDRVL--TELVAKMRE-MKMDKTELGCLRAIVLFNGLQAVQEVEQLREKVYASLEEYCKQRYGRFAKLLLRLPALRSIG Drosophila_melanogaster_USP CSICGDRASGKHYGVYSCEGCKGFFKRTV----RKDL--TYA-CRE-NR----NCIIDKRQRNR---CQYCRYQKCLTCGMKREVSALCQVVNKQLFQMVEYARMMPHFAQVPLDDQVILLKAAWIELLIANVAWCSIVSLIFDRIL--SELSVKMKR-LNLDRRELSCLKAIILYNGIKSRAEIEMCREKVYACLDEHCRLEHGRFAQLLLRLPALRSIS Crassostrea_gigas_NR2CD CVVCGDKASGRHYGCTSCEGCKGFFKRSI----RKQL--GYA-CRG-NK----DCPVNKPHRNR---CQYCRLQKCLAVGMRAEVHYICETASRLLFLSMHWTRSIPAFHVLSQEVQTILVKSSWSELFTLGLAQCAQSMSVIDHILKLQNYIQSLEA-LQIDSEEFAYLKALVLFSSLPNAPQIERVQDRAQRELANHVRQTHDRLAKLLLRLPALHSLS Caenorhabditis_elegans_NHR41 CVVCGDKASGRHYGAVSCEGCKGFFKRSI----RKRI--GYV-CRS-QK----DCPVTKFHRNR---CQYCRLRKCLSMGMRSEHQYISEITTRLLFLTVHFVKDSR--VSLRTSTMEGLLKSKWCDLYILALMQTADKIKQMQRLL---QLSQLFAS-RELTAVEYAYLKMISFTASSMASPETRSVNQMASQELFEYVSSSKERFSRILQLLPCLRWFD Homo_sapiens_TR2 CVVCGDKASGRHYGAVTCEGCKGFFKRSI----RKNL--VYS-CRG-SK----DCIINKHHRNR---CQYCRLQRCIAFGMKQDVHYIGESASRLLFLSMHWALSIPSFQALGQENSISLVKAYWNELFTLGLAQCWQVMNLMEHIFKLQEFCNSMVK-LCIDGYEYAYLKAIVLFSSLENMEQIEKFQEKAYVEFQDYITKTYYRLSRLLLRLPALRLMN Homo_sapiens_TR4 CVVCGDKASGRHYGAVSCEGCKGFFKRSV----RKNL--TYS-CRS-NQ----DCIINKHHRNR---CQFCRLKKCLEMGMKMEVHYICESASRLLFLSMHWARSIPAFQALGQDCNTSLVRACWNELFTLGLAQCAQVMSVMEHIWKLQEFCNSMAK-LDIDGYEYAYLKAIVLFSGLTSTSQIEKFQEKAQMELQDYVQKTYYRLARILVRLPALRLMS Drosophila_melanogaster_DHR78 CLVCGDRASGRHYGAISCEGCKGFFKRSI----RKQL--GYQ-CRG-AM----NCEVTKHHRNR---CQFCRLQKCLASGMRSDIHYVCETGSRIIFLTIHTLRKVPVFEQLEAHTQVKLLRGVWPALMAIALAQCSVPTILTRTLH---DFVQELQS-LDVTDMEFGLLRLILLFNTLLQQRKERSLRGYVRRVQLYALSSLRERFNVLVARLLPLSSLD Homo_sapiens_TLX CKVCGDRSSGKHYGVYACDGCSGFFKRSI----RRNR--TYV-CKS-GN--QGGCPVDKTHRNQ---CRACRLKKCLEVNMNKDTESVCESAARLLFMSIKWAKSVPAFSTLSLQDQLMLLEDAWRELFVLGIAQWAIPVDEIQALQ---EVVARFRQ-LRLDATEFACLKCIVTFKSFRNAAAIAALQDEAQLTLNSYIHTRYCRFGKLLLLLPALRSIS Drosophila_melanogaster_DSF CKVCGDRSSGKHYGIYSCDGCSGFFKRSI----HRNR--IYT-CKA-TGDLKGRCPVDKTHRNQ---CRACRLAKCFQSAMNKDWEMLQETTARLLFMAVRWVKCLMPFQTLSKNDQHLLLQESWKELFLLNLAQWTIPLDEMKTIQ---EILCRFRQ-ITPDGSEVGCMKAIALFAGLCDVQPVEMLQDQAQCILSDHVRLRYTRFGRLLLLLPSLRTIR Crassostrea_gigas_NR2E5 CLVCGDKASGKHYGVQSCDGCRGFFKRSI----RRSL--EYV-CKE-NG----NCVVDVARRNQ---CQACRFRKCLEMKMNRDNDCTFETAAKLLFMSVKWAKNIPSFLQLPFRDQAILLEESWCELFVLSAAQWSLNIDQLRQLQ---DIIYRLNG-IRLDSTEYACLKALLLFKGLRDSLQVEALQDQAQIMLYDYVSNQKTRFGRLLLQLPALRNVS Crassostrea_gigas_NR2E1 CKVCQDHSSGKHYGIYACDGCAGFFKRSI----RRNR--QYI-CKS-RG--QGTCPVDKTHRNQ---CRACRLKKCLEAGMNKDPEAMCEVAARLLFMSVKWAKNVPAFLGLPFRDQVMLLEEGWRELFVLGAAQFQMPVEEIRALQ---EIISKFKS-LQVDPTEFACLKGIVLFKSLQDIHTVAGLQDQAQLTLSKYIQATYFRFGKLLLSIPTLKTVC Crassostrea_gigas_NR2E2 CKVCQDHSSGKHYGIYACDGCAGFFKRSI----RRNR--QYV-CKS-RN--QDKCPVDKTHRNQ---CRACRLNKCVKSGMNRDADSVCETAARILFMTIKWTKSIPAFVGLPNRDQLVLIEESWRDLFILSLAQFRLPIQEIRALH---DVIDKFKL-INVDPTEYTCLKAIVIFKTLRDSHAVALLQDQAQVTLSKYIESTYFRFGKLLLLLPLLQTVS Drosophila_melanogaster_TLL CKVCRDHSSGKHYGIYACDGCAGFFKRSI----RRSR--QYV-CKS-QK--QGLCVVDKTHRNQ---CRACRLRKCFEVGMNKDAEHIKETAAEHLFKNVNWIKSVRAFTELPMPDQLLLLEESWKEFFILAMAQYLMPMNVTREVHAFQEVLNQLCH-LNIDSTEYECLRAISLFRGLLESGKVAAMHNDARSALHNYIQRTHMRFQTLLGVVQLMHKVS Drosophila_melanogaster_DHR51 CVVCGDTSSGKHYGILACNGCSGFFKRSV----RRKL--IYR-CQA-GT---GRCVVDKAHRNQ---CQACRLKKCLQMGMNKDHETVYETSARLLFMAVKWAKNLPSFARLSFRDQVILLEESWSELFLLNAIQWCIPLDDVRTLH---EIFCKYKA-VLVDPAEFACLKAIVLFRGLKDPAQIENLQDQAHVMLSQHTKTQFARFGRLLLMLPLLRMIS Crassostrea_gigas_NR2E3 CVVCGDTSSGKHYGILACNGCSGFFKRSV----RRKL--IYR-CQA-GT---GMCLVDKAHRNQ---CQACRLKKCLQMGMNKDQETMYECSARLLFVAIRWAKNLPSFANLPFRDQVILLEEAWSELFLLCAIQWSMPMEDNRLLQ---EIFRRFKH-TQVDPAEFACLKAIALFKGLKDPLQVENFQDQAQMMMSQHVRSNYIRFGRLLLMIPSLKFVP Drosophila_melanogaster_DHR83 CAVCGDQSSGKHYGVSCCDGCSCFFKRSV----RRGS--SYA-CIA-LV---GNCVVDKARRNW---CPSCRFQRCLAVGMNAAQALHFQILAQILVTCLRQAKANEQFALLDRCQQDAIFQVVWSEIFVLRASHWSLDIS-DEQLK---RLICEAHQ-LRADVLELNFMESLILCR-AINAEYAVILGSHSKAALISLARYTLLRFGQLLLGLRQ----- Caenorhabditis_elegans_FAX1 CAVCGDVSSGKHYGILACNGCSGFFKRSV----RRRL--IYR-CQA-GT---GNCVVDKAHRNQ---CQACRLKKCLNKGMNKDKDSLQETTMSQLESVLQWAQQFRLFTVLTNSEKRQIILTQWPRLLCISLCEQAEDVSFDDHLT---SLMLKFRR-LDVSPAEFNCLKAITIFM--RELSLWRAGWDNRASIITVYPAGERARLVAAALLLAEHSVMG Homo_sapiens_PNR CRVCGDSSSGKHYGIYACNGCSGFFKRSV----RRRL--IYR-CQV-GA---GMCPVDKAHRNQ---CQACRLKKCLQAGMNQDLDSIHETSARLLFMAVKWAKNLPVFSSLPFRDQVILLEEAWSELFLLGAIQWSLPLDETRVLQ---ETISRFRA-LAVDPTEFACMKALVLFKGLKDPEHVEALQDQSQVMLSQHSKAHHVRFGKLLLLLPSLRFIT Homo_sapiens_COUPTF1 CVVCGDKSSGKHYGQFTCEGCKSFFKRSV----RRNL--TYT-CRA-NR----NCPIDQHHRNQ---CQYCRLKKCLKVGMRREIENICELAARLLFSAVEWARNIPFFPDLQITDQVSLLRLTWSELFVLNAAQCSMPLHHIRIFQ---EQVEKLKA-LHVDSAEYSCLKAIVLFTGLSDAAHIESLQEKSQCALEEYVRSQYSRFGKLLLRLPSLRTVS Homo_sapiens_COUPTF2 CVVCGDKSSGKHYGQFTCEGCKSFFKRSV----RRNL--SYT-CRA-NR----NCPIDQHHRNQ---CQYCRLKKCLKVGMRREIENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHHIRIFQ---EQVEKLKA-LHVDSAEYSCLKAIVLFTGLSDVAHVESLQEKSQCALEEYVRSQYTRFGKLLLRLPSLRTVS Homo_sapiens_EAR2 CVVCGDKSSGKHYGVFTCEGCKSFFKRSI----RRNL--SYT-CRS-NR----DCQIDQHHRNQ---CQYCRLKKCFRVGMRKEIDNVCELAARLLFSTVEWARHAPFFPELPVADQVALLRLSWSELFVLNAAQAALPLHQVRAFQ---EQVDKLGR-LQVDSAEYGCLKAIALFTGLSDPAHVESLQEKAQVALTEYVRAQYQRFGRLLLRLPALRAVP Drosophila_melanogaster_SVP CVVCGDKSSGKHYGQFTCEGCKSFFKRSV----RRNL--TYS-CRG-SR----NCPIDQHHRNQ---CQYCRLKKCLKMGMRREIDNICELAARLLFSAVEWAKNIPFFPELQVTDQVALLRLVWSELFVLNASQCSMPLHHIRIFQ---EQVEKLKA-LHVDSAEYSCLKAIVLFTGLSDVTHIESLQEKSQCALEEYCRTQYTRFGKLLLRLPSLRTVS Caenorhabditis_elegans_UNC55 CVVCGDKSSGKHYGQFSCEGCKSFFKRSI----RRSL--SYT-CRA-TK----NCAIDVQHRNQ---CQYCRLTKCIRMGMRKEKESIFEFAAQTIFATVNWART--SMSNLVKGDQLILLRHSWTPIFIFALAQSNFALNQFQGFQ---AKIDKIRD-FHLDVVESSSLRAVLLFSALEEKGKIEEIVEKLKSAVDEYCKMNKERYHQICECLQLLKST- Crassostrea_gigas_NR2F CVVCGDKSSGKHYGQFTCEGCKSFFKRSV----RRNL--TYT-CRG-SR----QCPIDQHHRNQ---CQYCRLKKCLKMGMRREIENICELAARLLFSAVEWARNIPFFPELQITDQVALLRVSWSELFVLNAAQCSMPLHHIRIFQ---EQVEKLKT-LHVDSAEYSCLKAIVLFSGLSDATHIENIQEKSQCALEEYVRSQYTRFGKLLLRLPSLRTVS Homo_sapiens_ERa CAVCNDYASGYHYGVWSCEGCKAFFKRSI----QGHN--DYM-CPA-TN----QCTIDKNRRKS---CQACRLRKCYEVGMMKGMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPIFDMLL---ATSSRFRM-MNLQGEEFVCLKSIILLNSLEEKDHIHRVLDKITDTLIHLMAKAGQRLAQLLLILSHIRHMS Homo_sapiens_ERb CAVCSDYASGYHYGVWSCEGCKAFFKRSI----QGHN--DYI-CPA-TN----QCTIDKNRRKS---CQACRLRKCYEVGMVKCMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPIFDMLL---ATTSRFRE-LKLQHKEYLCVKAMILLNDADSSRKLAHLLNAVTDALVWVIAKSGMRLANLLMLLSHVRHAS Mytilus_edulis_ER CQVCSDNASGFHYGVWSCEGCKAFFKRSI----QGPV--DYV-CPA-TN----SCTIDKHRRKS---CQACRLRKCYEVGMNKGLNSLVKLAERELVQLINWAKNVPGYIDLSLSDQVHLIECCWMELLLLNCTFRSMSYNIFEQVS---AVSENFIQ-YQLHKNESLLLQATVLVNRLTSCDKIHRMRQSILDAVVDTAQKYHRHVPSILLMLTHIRQAG Crassostrea_gigas_ER CQVCSDNASGFHYGVWSCEGCKAFFKRSI----QGPV--DYV-CPA-TN----TCTIDKHRRKS---CQACRLRKCYEVGMNKGLNSLVKLAERELVHLINWAKNVPGYTDLSLSDQVHLIECCWMELLLLNCAFRSIEHGIFEQVA---AVSEQMMQ-NHLHKDELLLLQAMVLVNRLASYNQIFNMQQSLLDAIVDTAQKYHRHVPAVLLLLTHIRQAG Octopus_vulgaris_ER CQVCDDNASGFHYGVWSCEGCKAFFKRSI----QGPV--DYV-CPA-TN----SCTIDKHRRKS---CQACRLRKCYEVGMNKGLQLLIQVADKDLVQLINWAKHIPGYADLSLSDQVHLIECCWMELVLLNCAYRSMEYEILEQVA---AVSEQLLQ-FGINREELLLLEATILVNRLAGFSKIDDIRQIILNALIDTAQKYHRHVPSALLLLSHVRQAS Aplysia_californica_ER CQVCSDNASGFHYGVWSCEGCKAFFKRSI----QGPV--DYI-CPA-TN----TCTIDKHRRKS---CQACRLRRCYEVGMNKGLNTLIKLADRELVYLINWAKHVPGYTCLTLGDQVHLIECCWMELLLLNCAFRSMEHEVLEQVS---AVSEQMLL-HGLNKEELLLLQATVLVNPLDSFLKIQEMRQLILDVFMEVAGRHQRHAPSILLLLTHIRQAG Thais_clavigera_ER CQVCNDNASGFHYGVWSCEGCKAFFKRSI----QGPV--DYM-CPA-TN----NCTIDKHRRKS---CQACRLRKCYEVGMNKGLNTLIKLADRELVYLINWAKHVPGYTDLSLSDQVHLIECCWMELLLLNCAFRSMDYDILEQVS---AVTEQMVH-YAVTKEEQLLLKATILVNRLASFDKIMEMRQMIVDALMEVAQKSHRRVPSLLLLLTHVRQAG Marisa_cornuarietis_ER CQVCNDNASGFHYGVWSCEGCKAFFKRSI----QGPV--DYM-CPA-TN----NCTIDKHRRKS---CQACRLRKCYEVGMNKGLNTLIKLADRELVYLINWAKHVPGYTDLSLSDQVHLIECCWMELLLLNCAFRSMDHEILEQVG---AVSEQMVQ-YSVSKEELLLLQATVLVNRLASYSKIGEMQQMIVDALMDIAQRTHRHVPSLILLLTHIRQAG Nucella_lapillus_ER CQVCNDNASGFHYGVWSCEGCKAFFKRSI----QGPV--DYM-CPA-TN----NCTIDKHRRKS---CQACRLRKCYEVGMNKGLNTLIKLADRELVYLINWAKHVPGYTDLSLSDQVHLIECCWMELLLLNCAFRSMDYDILEQVS---AVTEQMVQ-YTVTKEELLLLKATILVNRLASMDKIVEMRQMIVDALTEVAQKSHRRVPCLLLLLTHVRQAG Crassostrea_gigas_NR3A CQVCSDNASGFHYGVWSCEGCKAFFKRSI----QGPV--DYV-CPA-TN----TCTIDKHRRKS---CQACRLRKCYEVGMNKGLNSLVKLAERELVHLINWAKNVPGYTDLSLSDQVHLIECCWMELLLLNCAFRSIEHGIFEQVA---AVSEQMMQ-NHLHKDELLLLQAMVLVNRLASYNQIFNMQQSLLDAIVDTAQKYHRHVPAVLLLLTHIRQAG Homo_sapiens_ERRa CLVCGDVASGYHYGVASCEACKAFFKRTI----QGSI--EYS-CPA-SN----ECEITKRRRKA---CQACRFTKCLRVGMLKEVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQLGAALL---QLVRRLQA-LRLEREEYVLLKALALANHIEDAEAVEQLREALHEALLEYEAGRARRAGRLLLTLPLLRQTA Homo_sapiens_ERRb CLVCGDIASGYHYGVASCEACKAFFKRTI----QGNI--EYS-CPA-TN----ECEITKRRRKS---CQACRFMKCLKVGMLKELTTLCDLADRELVVIIGWAKHIPGFSSLSLGDQMSLLQSAWMEILILGIVYRSLPYDLYRAIL---QLVRRYKK-LKVEKEEFVTLKALALANYIEDLEAVQKLQDLLHEALQDYELSQRWRTGKLLLTLPLLRQTA Homo_sapiens_ERRg CLVCGDIASGYHYGVASCEACKAFFKRTI----QGNI--EYS-CPA-TN----ECEITKRRRKS---CQACRFMKCLKVGMLKELTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFELNNAIL---QLVKKYKS-MKLEKEEFVTLKAIALANHIEDVEAVQKLQDVLHEALQDYEAGQHRRAGKMLMTLPLLRQTS Marisa_cornuarietis_ERR CLVCGDVASGYHYGVSSCEACKAFFKRTI----QGNI--EYS-CPA-SG----ECEITKRRRKA---CQACRFQKCLRVGMLRERAAVSDLADRELVITISWAKQVPGFTNLSLMDQMNLLQHSWLEILCLNLVFRSCPYNLDSLTR---KLCKKFTY-LGVSKEEYVLLKAIILCNVVETGETVRGLQDKLQDSLIECIKARHRRLGQLFLLLPPITHIK Crassostrea_gigas_NR3B CLVCGDVASGYHYGVSSCEACKAFFKRTI----QGNI--EYS-CPA-NG----DCEITKRRRKA---CQACRFQKCLRVGMLRELATVSDLADRELVITISWAKQVPGFCTLSLSDQMNLLQHSWLEILCLNLVFRSCPYNLDGISR---KLAKKFTD-MEVTKEEYLLLKAMTLCNAIENSEAVRQLQDKLQDSLIEYVKYRYRRLGHLYMLLPALNHMK Drosophila_melanogaster_DERR CLVCGDVASGFHYGVASCEACKAFFKRTI----QGNI--EYT-CPA-NN----ECEINKRRRKA---CQACRFQKCLLMGMLKELSVLSDIYDKELVSVIGWAKQIPGFIDLPLNDQMKLLQVSWAEILTLQLTFRSLPFNFYYHCV---QIAQRMER-ISPRREEYYLLKALLLANLLDDQSSLRAFRDTILNSLNDVVYLLRSHQQQLLLLLPSLRQAD Homo_sapiens_GR CLVCSDEASGCHYGVLTCGSCKVFFKRAV----EGQH--NYL-CAG-RN----DCIIDKIRRKN---CPACRYRKCLQAGMNLEMTTLNMLGGRQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMAFALGWRSYRQSQCKHML---YVSSELHR-LQVSYEEYLCMKTLLLLSGLKSQELFDEIRMTYIKELGKAIVKREQRFYQLTKLLDSMHEVV Homo_sapiens_MR CLVCGDEASGCHYGVVTCGSCKVFFKRAV----EGQH--NYL-CAG-RN----DCIIDKIRRKN---CPACRLQKCLQAGMNLGLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMCLSSFALSWRSYKHTLCQGMH---QISLQFVR-LQLTFEEYTIMKVLLLLSGLKSQAAFEEMRTNYIKELRKMVTKCPQRFYQLTKLLDSMHDLV Homo_sapiens_PR CLICGDEASGCHYGVLTCGSCKVFFKRAM----EGQH--NYL-CAG-RN----DCIVDKIRRKN---CPACRLRKCCQAGMVLGLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVLCLTMW---QIPQEFVK-LQVSQEEFLCMKVLLLLNGLRSQTQFEEMRSSYIRELIKAIGLRQQRFYQLTKLLDNLHDLV Homo_sapiens_AR CLICGDEASGCHYGALTCGSCKVFFKRAA----EGKQ--KYL-CAS-RN----DCTIDKFRRKN---CPSCRLRKCYEAGMTLGLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVQCVRMR---HLSQEFGW-LQITPQEFLCMKALLLFSGLKNQKFFDELRMNYIKELDRIIACKRRRFYQLTKLLDSVQPIA Crassostrea_gigas_NR4A CAVCGDNAACQHYGVRTCEGCKGFFKRTV----QKNA--KYV-CLA-DK----NCPVDKRRRNR---CQFCRFQKCLSVGMVKETQMFYDLITSSVNIIKAWSTKIPGFSDICQEDQNLLFKSASLELFVLRLSYRMQGNTWINSIA---DFSTSLYR-MSLDISALACMEALTLVTGLKNQAKMEEVQMKIIDSLRDHCVYNSNYFSSILGKVAELRTLS Drosophila_melanogaster_DHR38 CAVCGDTAACQHYGVRTCEGCKGFFKRTV----QKGS--KYV-CLA-DK----NCPVDKRRRNR---CQFCRFQKCLVVGMVKEVQQFYQLLTSSVDVIKQFAEKIPGYFDLLPEDQELLFQSASLELFVLRLAYRARIDDWLNDIM---EFSRSLHN-LEIDISAFACLCALTLITGLREPKKVEQLQMKIIGSLRDHVTYNAHYFSRLLGKLPELRSLS Caenorhabditis_elegans_NHR6 CAVCNDRAVCLHYGARTCEGCKGFFKRTV----QKNS--KYT-CAG-NK----TCPIDKRYRSR---CQYCRYQKCLEVGMVKEETIALRILHGELHATKKLLMAMPQISEIQPADFQILLSRSFFAIMAIRVANRCGNSTIIRFMV---DKARTFSSLVDWEPQAFAAFIALQFLAGLTNKPLVDQVQSTIINALKDHCSGSQNKLAKIVRLTQEFDVFH Homo_sapiens_NGFIB CAVCGDNASCQHYGVRTCEGCKGFFKRTV----QKNA--KYI-CLA-NK----DCPVDKRRRNR---CQFCRFQKCLAVGMVKEVQQFYDLLSGSLEVIRKWAEKIPGFAELSPADQDLLLESAFLELFILRLAYRSKPGEWIDSIL---AFSRSLHS-LLVDVPAFACLSALVLITGLQEPRRVEELQNRIASCLKEHVAAVASCLSRLLGKLPELRTLC Homo_sapiens_NURR1 CAVCGDNAACQHYGVRTCEGCKGFFKRTV----QKNA--KYV-CLA-NK----NCPVDKRRRNR---CQYCRFQKCLAVGMVKEIQQFYDLLTGSMEIIRGWAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSNPVEWIDSIV---EFSSNLQN-MNIDISAFSCIAALAMVTGLKEPKRVEELQNKIVNCLKDHVTFNNNYLSKLLGKLPELRTLC Homo_sapiens_NOR1 CAVCGDNAACQHYGVRTCEGCKGFFKRTV----QKNA--KYV-CLA-NK----NCPVDKRRRNR---CQYCRFQKCLSVGMVKEVQQFYNLLTASIDVSRSWAEKIPGFTDLPKEDQTLLIESAFLELFVLRLSIRSNTAEWLDSIK---DFSLNLQS-LNLDIQALACLSALSMITGLKEPKRVEELCNKITSSLKDHQSKGQ-TESKVLGALVELRKIC Homo_sapiens_SF1 CPVCGDKVSGYHYGLLTCESCKGFFKRTV----QNNK--HYT-CTE-SQ----SCKIDKTQRKR---CPFCRFQKCLTVGMRLEFGLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQHGLVLRAQ---ELVLQLLA-LQLDRQEFVCLKFIILFSFLNNHILVKDAQEKANAALLDYTLCHYDKFQQLLLCLVEVRALS Homo_sapiens_LRH CPVCGDKVSGYHYGLLTCESCKGFFKRTV----QNNK--RYT-CIE-NQ----NCQIDKTQRKR---CPYCRFQKCLSVGMKLEFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGLMSHAQ---ELVAKLRS-LQFDQREFVCLKFLVLFSNLENFQLVEGVQEQVNAALLDYTMCNYEKFGQLLLRLPEIRAIS Crassostrea_gigas_NR5B CPVCGDNVSGYHYGIFTCESCKGFFKRTV----QNNK--TFT-CHR-NG----DCEISRGNRKK---CPSCRFAKCVLMGMKTQIMSMLQLAELKLYKLVRWARNLPQFSSIATDDQILLLQNSWCEILTLNCCFKSMNTPIISRML---SIAEHLRR-LQVDQHEFVALKVLILISGMKEPSRVVEHQDAITEALRQYTESHFTKYGQLLMRLTELAKI- Caenorhabditis_elegans_NHR25 CPVCGDRVSGYHYGLLTCESCKGFFKRTV----QNKK--QYQ-CSA-EA----NCHVDRTCRKR---CPSCRFQKCLTMGMKMEHAFSIQVAEENLKDIVIWAKNDQLFSKLSLDDQMILLQTSWTTVHIVDITNAMVHGNFVSSWN---DVVIRLRN-MGFTNFDYCAFRFLALF-MDSFPAVSTARSRVLQSWREVRCTTAFLEIFEQIRRL------- Drosophila_melanogaster_FTZF1 CPVCGDKVSGYHYGLLTCESCKGFFKRTV----QNKK--VYT-CVA-ER----SCHIDKTQRKR---CPYCRFQKCLEVGMKLEFELMCKVLDQNLFSQVDWARNTVFFKDLKVDDQMKLLQHSWSDMLVLDHLHHRIHNGLGDYFN---ELQNKLQD-LKFDMGDYVCMKFLILLNGIVNRKTVSEGHDNVQAALLDYTLTCYDKFRGLVNILPEIHAMA Drosophila_melanogaster_DHR39 CPICGDKISGFHYGIFSCESCKGFFKRTV----QNRK--NYV-CVR-GG----PCQVSISTRKK---CPACRFEKCLQKGMKLEIAHLCNVADHRLYKIVKWCKSLPLFKNISIDDQICLLINSWCELLLFSCCFRSIDTPCIERML---NLTDHLRR-LRVDRYEYVAMKVIVLLQELQEAVKVRECQEKALQSLQAYTLAHYSKFGELLLRIPDLQRT- Crassostrea_gigas_NR5A CPVCGDKVSGYHYGLLTCESCKGFFKRTV----QNKK--VYS-CVD-NR----NCHIDKSQRKR---CPYCRFQKCLSVGMKLEINMLCKLSDQLLFLMVEWARTSFFFKDLKVEDQMKLLQNCWSEILILDLVHRLVRETAKESIF---DLVRKMKE-LKIDVNEYLCLKFLILLNGLENRQAVENSQEKVNSALMEYCVNFYDKFGQVLLRLPEVRLIS Caenorhabditis_elegans_NHR91 CSVCGDKSTGLHYGAATCEGCKGFFKRSV----QNKK--VYH-CSQ-DN----CCEIDKQNRNR---CQSCRFRKCISKGMLTECKRLTRIGDEIVEQLVEWTKTLPFFDELPVEAHTHLLTQRWAELVLLSAGYYMIDETLVTRFT---TLLHSFSN-LKVSPEAYVCIKAITLLH-----DKVNTLQDHFVKTLQIHLHQPGTSLAQILDWLPDLRNAS Drosophila_melanogaster_DHR4 CMICEDKATGLHYGIITCEGCKGFFKRTV----QNRR--VYT-CVA-DG----TCEITKAQRNR---CQYCRFKKCIEQGMVLQSEKLCNIGDSIVHKLVSWTKKLPFYLEIPVEIHTKLLTDKWHEILILTTAAYLQPLHMVDKMT---QITIMFRR-IKLKMEEYVCLKVYILLN-----VELESIQERYVQVLRSYLQNSSARLSELLSHIPEIQAAA Homo_sapiens_GCNF CLICGDRATGLHYGIISCEGCKGFFKRSI----CNKR--VYR-CSR-DK----NCVMSRKQRNR---CQYCRLLKCLQMGMNRKFALLCRLADELLFRQIAWIKKLPFFCELSIKDYTCLLSSTWQELILLSSLTVYSKQIVIERLI---YLYHKFHQ-LKVSNEEYACMKAINFLNGLTSASQLEQLNKRYWYICQDFTEYKYNRFPDLMMCLPEIRYIA Crassostrea_gigas_NHR43 CHVCQDQATGVHYGVATCEGCKGFFKRST----IRGE--KYK-CFF-GG----QCEITPQNRNR---CKSCRFRLCLESGMSLEWPNLMQSVQFYNDVILGFAFGCPGFKNLQSELKEILTQNAYFEIWIL-LMADFCIDGSVVEIK---GVLEKINK-CQLCDLEIGLLCAILLIDTVVTKIHTTQSTKKLSDIFSLTPLIKKSTLLRLQVTQYGVEQVP Crassostrea_gigas_NR1P7 CRICGGKASGIHYGVNSCEACKGFFRRYL----LRKE--PYK-CNH-GG----NCAITNRHRGN---CSACRMMKCLDLGMSKELQFNKGTLDNMIKKYVNFSHAIPCFSDLPSQDQAKLLKASRFEFFMLLEYRSLNPDLMMKSWL---EFSRTIRK-LELTNKELAVTLAVALTFRLEQPSFLEQIQDNLVRMLYYLLEDHHVAFSRIISMLTGLRSLT Crassostrea_gigas_NR1P1 CRICGKRASGIHFGVYSCEACKAFFRRCL----QRTS--PYK-CDK-GG----NCIIDEQQKGLN--CSACRLKKCQELGMSKELQDGRRDMVQIVKEYVQFTHGIPNFKTLSPKDQSTLLKASRFEFFAILQYRALDSERVFRGWF---EFARRVKE-CDFSQEEHALVLAISLTFSLEEPDKVEEIQTKLIDSLENLLKETHRRLAKIMDLFVRLRALG Crassostrea_gigas_NR1P3 CRICGKRASGIHFGVYSCEACKAFFRRYL----QRKT--PFK-CNK-GD----KCEIDEQKKGLN--CSACRLKKCLEKGMSKEYDLGREELNKMFDELVQFTHSIVNFSSLPSKDQTALLKAADFDFNMLVDYRCVDADRTLKEWA---EFSRSLQK-LKLTPREHALMLAISLTFPLEAHDEVEKIQNKLIKALEKLVAETNGRFAKLMDVFLRMRGMY Crassostrea_gigas_NR1P8 CKVCSGNATGIHYGVHTCEPCKAFFRRAI----TDKN--KYA-CLK-EN----SCEITAQKRGN---CSACRLQKCFDLGMSKSIKKIFSHRERSLMKFITFAKCLEGFNTLSMNDKINLVKYGEHEYWVLGHFTHYHPEIASEELL---KMFCTLKD-MDLMYQEVIILRGIVLFSELESAPIVESVQWKLIQCLQYLVEHFHRKFSQCLQLLTDLREVS Crassostrea_gigas_NR1P9 CRICDGEASGIHYGVNTCEACKAFFRRAV----MEKD--KYQ-CAK-DK----NCKIIDRKRGN---CSYCRLQKCLNLGMSRDIKKAIEQIQHGIMKYISFARIIPGFEDLPTDDKMALIKAARFEYWLMGEHVHINTEMAVDRCI---EFAASLQR-LKLTYEEVAVLKAIIITFPLQNPEKVETIQWKLVQCLKYLIAKFHHRFSAYMDKLIFMRELT Crassostrea_gigas_NR1P6 CKICGKKASGIHYGVNTCEACKGFFRRYL----KRKE--PYV-CDK-GW----NCDLDIRSKGPH--CSACRMKKCLTLGMSKESSRRREEFGLAMADYVAFSNEIPGFNELSARDKATLVKVSRLDFFLSLEYRAKDPETMLRSWW---KLTYDLRG-LQMTTEEHATLLALCLMSKLESPESVQKIEATLVKTMMSLLHRRYLQFSSYISLLTKLRGMS Crassostrea_gigas_NR1P4 CKICGKKASGNHYGVNSCEACKGFFRRYL----QRNV--PYK-CNK-GG----KCLENSDNKKNSL-CSACRMQKCLDCGMCREFEVIRDELGILVQEYVRFTHGLPGFSDLPPTDQAKLLKAARLEFFFILGYRSFDSETMAVKWV---NISDDVRN-LSLTTQEHAVILAICLTFDLDARDKVEEIQMLFIDALQYLLKKRLLHFSRIMNVFLKLREMN Crassostrea_gigas_NR1P5 CRICGKLASGIHYGVNSCEACKGFFRRYL----KRKE--PFQ-CTK-GG----NCVIDQSSAGSM--CSGCRLQKCFSLGMSKEFDLIRQELVTVIHEYVRFTHGIPAFQNLPSKDQASLLKAARLEFFLLLGYRSLDPETMSTSWL---EVTRHIRH-LQLHPKEHAAMLGICLTFPLEDPKSVEKIQTCLLGVLQNMLRVRYRHLARIMDVFIKLRGLN Crassostrea_gigas_NR1P2 CRVCGKKSTGIHFGVYSCEACKTFFRRSF----LRST--PYK-CDK-GG----DCLINAEKQNGSRPCPACRLVKCLDLGMSKDLSEAKYEFMKMANDYIKFCKNIPFFSGLSLEDQKALLKCSHFEFFTILQHKGMNTEKTLLSWA---EFSEEVSK-LQLSPEEFALMLGICVTFPLDYPEDVENIQKRLLETLEFTLSKSHRRLAKLLDLFVRLRVIG Crassostrea_gigas_NR1P10 CRVCGEKASGFHYGVNTCEACKGFFRRSL----RRKT--EYK-CVKSDK----NCTIAPGKRNG---CPLCRYNKCLAVGMSKEVSNFATNMEKSITKFVTFTKTIPGFAALPLEDQANLVKSSRFEFWMFGFWKFIDVENFVEALF---NFGQTLHN-LQMSDLEIALVRCICLTYELKSPEKVEEIQWKMIMCLKYIIEKNHRYLSRIMDRLAAVRNLT Mytilus_galloprovincialis_NR1G CRVCGQKASGFHYGANTCEACKGFFRRSIVKIIKKKE--TYK-CSK-DK----NCPIGPGRRAM---CAFCRYKKCLDIGMSQEMGKIATSMEKNIRNIVEFVRLIPGYSQLSTKDRLQLIKSCFSDYWFLAAHKRINLELYLDEIC---QVTTKLQK-CNMTIEEVTLLRAITLTADLENPAKVEEIQWKLISFLRSLLKKSYQRLWQLFDIMTSLRNL- Crassostrea_gigas_NR1P11 CRVCGDNASGFHYGANTCEACKGFFRRSIVKIQQNKE--SYK-CIAKGE----GCVLGPGKRNP---CAACRYARCLEVGMSIGMKEMACRMEHGLTMMVDFVRTIPGFADLSVSDQTELIKASHFEFFFLVHHKSFNPDLAVENLF---QFSTSLKN-LDLAFDEIILVRGISVTFQLEDPKAVEQIQWRLINALRVLAKRKNQRLWHILDRLTALRTMT Crassostrea_gigas_NHR42 CMICNDRGSGYHYSVFSCEGCKGFFKRSV----QKNL--VYT-CKN-EG----SCVINKFTRNN---CQYCRFVKCTQMGMKREINQLMQYGYAELKYIIDWAKKVPGFTELRLEDQMALLKSSFMELNVLRLSYRSMETGLVAATV---EFSARLKE-LSIDKVEFCILNGIVLTYNLMDKQKVILLQTQILDRLRKYHSHKFRRYGKMLLRLPFLRTVS ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 221; END; BEGIN TREES; Title 'Trees from "DBDLBD_ML.nex"'; LINK Taxa = 'Species_list_nuclear_receptors'; TRANSLATE 1 Homo_sapiens_THRa, 2 Homo_sapiens_THRb, 3 Crassostrea_gigas_NR1A, 4 Crassostrea_gigas_NR1B, 5 Homo_sapiens_RARa, 6 Homo_sapiens_RARb, 7 Homo_sapiens_RARg, 8 Lymnaea_stagnalis_RAR, 9 Homo_sapiens_PPARa, 10 Homo_sapiens_PPARb, 11 Homo_sapiens_PPARg, 12 Crassostrea_gigas_NR1C, 13 Homo_sapiens_Reverba, 14 Homo_sapiens_Reverbb, 15 Mytilus_galloprovincialis_NR1Dv1, 16 Crassostrea_gigas_NR1D, 17 Caenorhabditis_elegans_NHR85, 18 Drosophila_melanogaster_E75, 19 Crassostrea_gigas_NR1CDEFa, 20 Crassostrea_gigas_NR1CDEFb, 21 Mytilus_galloprovincialis_NR1DEF, 22 Crassostrea_gigas_NR1E, 23 Drosophila_melanogaster_E78, 24 Caenorhabditis_elegans_SEX1, 25 Homo_sapiens_RORa, 26 Homo_sapiens_RORb, 27 Homo_sapiens_RORg, 28 Crassostrea_gigas_NR1F, 29 Caenorhabditis_elegans_NHR23, 30 Drosophila_melanogaster_DHR3, 31 Homo_sapiens_LXRb, 32 Homo_sapiens_LXRa, 33 Crassostrea_gigas_NR1H, 34 Drosophila_melanogaster_EcR, 35 Homo_sapiens_FXR, 36 Homo_sapiens_VDR, 37 Homo_sapiens_PXR, 38 Homo_sapiens_CAR, 39 Drosophila_melanogaster_DHR96, 40 Caenorhabditis_elegans_DAF12, 41 Caenorhabditis_elegans_NHR8, 42 Crassostrea_gigas_NR1Ja, 43 Crassostrea_gigas_NR1Jb, 44 Crassostrea_gigas_NR1Jg, 45 Crassostrea_gigas_NR2A, 46 Caenorhabditis_elegans_NHR64, 47 Caenorhabditis_elegans_NHR69, 48 Homo_sapiens_HNF4a, 49 Homo_sapiens_HNF4b, 50 Drosophila_melanogaster_HNF4, 51 Crassostrea_gigas_NR2B, 52 Homo_sapiens_RXRa, 53 Homo_sapiens_RXRb, 54 Homo_sapiens_RXRg, 55 Lymnaea_stagnalis_RXR, 56 Biomphalaria_glabrata_RXR, 57 Thais_clavigera_RXR, 58 Nucella_lapillus_RXR, 59 Drosophila_melanogaster_USP, 60 Crassostrea_gigas_NR2CD, 61 Caenorhabditis_elegans_NHR41, 62 Homo_sapiens_TR2, 63 Homo_sapiens_TR4, 64 Drosophila_melanogaster_DHR78, 65 Homo_sapiens_TLX, 66 Drosophila_melanogaster_DSF, 67 Crassostrea_gigas_NR2E5, 68 Crassostrea_gigas_NR2E1, 69 Crassostrea_gigas_NR2E2, 70 Drosophila_melanogaster_TLL, 71 Drosophila_melanogaster_DHR51, 72 Crassostrea_gigas_NR2E3, 73 Drosophila_melanogaster_DHR83, 74 Caenorhabditis_elegans_FAX1, 75 Homo_sapiens_PNR, 76 Homo_sapiens_COUPTF1, 77 Homo_sapiens_COUPTF2, 78 Homo_sapiens_EAR2, 79 Drosophila_melanogaster_SVP, 80 Caenorhabditis_elegans_UNC55, 81 Crassostrea_gigas_NR2F, 82 Homo_sapiens_ERa, 83 Homo_sapiens_ERb, 84 Mytilus_edulis_ER, 85 Crassostrea_gigas_ER, 86 Octopus_vulgaris_ER, 87 Aplysia_californica_ER, 88 Thais_clavigera_ER, 89 Marisa_cornuarietis_ER, 90 Nucella_lapillus_ER, 91 Crassostrea_gigas_NR3A, 92 Homo_sapiens_ERRa, 93 Homo_sapiens_ERRb, 94 Homo_sapiens_ERRg, 95 Marisa_cornuarietis_ERR, 96 Crassostrea_gigas_NR3B, 97 Drosophila_melanogaster_DERR, 98 Homo_sapiens_GR, 99 Homo_sapiens_MR, 100 Homo_sapiens_PR, 101 Homo_sapiens_AR, 102 Crassostrea_gigas_NR4A, 103 Drosophila_melanogaster_DHR38, 104 Caenorhabditis_elegans_NHR6, 105 Homo_sapiens_NGFIB, 106 Homo_sapiens_NURR1, 107 Homo_sapiens_NOR1, 108 Homo_sapiens_SF1, 109 Homo_sapiens_LRH, 110 Crassostrea_gigas_NR5B, 111 Caenorhabditis_elegans_NHR25, 112 Drosophila_melanogaster_FTZF1, 113 Drosophila_melanogaster_DHR39, 114 Crassostrea_gigas_NR5A, 115 Caenorhabditis_elegans_NHR91, 116 Drosophila_melanogaster_DHR4, 117 Homo_sapiens_GCNF, 118 Crassostrea_gigas_NHR43, 119 Crassostrea_gigas_NR1P7, 120 Crassostrea_gigas_NR1P1, 121 Crassostrea_gigas_NR1P3, 122 Crassostrea_gigas_NR1P8, 123 Crassostrea_gigas_NR1P9, 124 Crassostrea_gigas_NR1P6, 125 Crassostrea_gigas_NR1P4, 126 Crassostrea_gigas_NR1P5, 127 Crassostrea_gigas_NR1P2, 128 Crassostrea_gigas_NR1P10, 129 Mytilus_galloprovincialis_NR1G, 130 Crassostrea_gigas_NR1P11, 131 Crassostrea_gigas_NHR42; TREE 'tree 1+' = ((((3:0.2706185164,(1:0.0971182646,2:0.030189519):0.3833037608):0.2876040176,(((31:0.2122647502,32:0.1093024458):0.3410034552,(35:0.6199893358,(33:0.5199104312,34:0.4347906793):0.129828496):0.0660818669):0.2472792415,((36:0.4049945634,(37:0.3012397091,38:0.4939841564):0.2449877619):0.1238358686,(44:0.6499930315,((42:0.4923814183,43:0.3975634756):0.1057942609,(39:0.456074738,(40:0.763400055,41:0.980352617):0.3196131831):0.1872018611):0.1566280817):0.4653864702):0.2809716063):0.2080584511):0.0872176253,(((4:0.1049921306,8:0.1491908364):0.0995997316,(7:0.0462613,(5:0.0564935734,6:0.0312641236):0.0234622147):0.2235588314):0.224625831,(((128:0.4777667889,(129:0.5240841763,130:0.4993315242):0.177952758):0.0871325262,((122:0.8390747198,123:0.2858107078):0.2806538259,(119:0.3162333723,((121:0.3572172372,(120:0.2263795563,127:0.6895675798):0.1689557593):0.2320632755,(124:0.7104783037,(125:0.4518378449,126:0.3299951805):0.0625020558):0.0860283697):0.1856736435):0.4618481684):0.1448309879):0.5813552375,(((27:0.293239517,(25:0.1375230783,26:0.1763280818):0.0374158716):0.2118871619,(28:0.2655875353,(29:0.8350309192,30:0.3055965127):0.1262815077):0.2221797582):0.2353131147,((22:0.2259303521,23:0.3727351548):0.2742156351,((24:0.9856897337,(17:1.214400263,118:2.2622926449):0.111867):0.4086160497,((20:0.6359677536,(19:0.4062651359,21:0.114833832):0.575068773):0.1672068474,((12:1.0412686628,(11:0.1416048817,(9:0.1531761184,10:0.1313565685):0.0987708787):0.4745021059):0.2997161806,((13:0.1218245383,14:0.0549695936):0.2678827079,(18:0.4286389401,(15:0.1080083652,16:0.0810793514):0.0649780503):0.1383447514):0.0520096903):0.0510088912):0.0604267982):0.0299190473):0.0990669986):0.2072308086):0.1625041453):0.0167896799):0.1352898437,((104:1.3148924563,((102:0.2841043324,103:0.1434671714):0.1011321031,(105:0.1953209766,(106:0.0687513687,107:0.2576781625):0.0527805778):0.0496273595):0.1641488287):0.4188235937,(131:0.7509522906,(((97:0.5474231873,((95:0.1397521958,96:0.0823529591):0.2768726444,(92:0.1993266576,(93:0.0954986627,94:0.0494145297):0.0960986854):0.1977816627):0.0682084318):0.2300498621,(((98:0.2017408562,99:0.2004528322):0.0490417079,(100:0.1481346486,101:0.3724628307):0.0463973928):1.0335811723,((82:0.1530401787,83:0.2582093139):0.2045243631,((88:0.0135262363,90:0.0233196552):0.0261421581,(89:0.0400379914,(87:0.1266470842,(86:0.1821192469,(84:0.091961384,(85:1.0E-10,91:1.0E-10):0.0752249615):0.0802451587):0.0246976397):0.056177664):0.0357371276):0.361036145):0.2212253212):0.2357209399):0.3944428429,(((117:0.7777906034,(115:0.674348352,116:0.5907984378):0.3312260632):0.3449649213,((110:0.4343260552,113:0.4243525606):0.3395961745,(114:0.2672475863,((108:0.3227320375,109:0.0446560707):0.1687431273,(111:1.3988727955,112:0.241457601):0.1873197738):0.073661977):0.3493599209):0.1981994954):0.1895156815,((((46:0.5660841495,47:0.5077127582):0.3489822625,((45:0.085303427,50:0.2056808283):0.0415327535,(48:0.0784496817,49:0.051810552):0.0951052882):0.1647371616):0.3729811237,(59:0.4202411373,((52:0.0090673703,(53:0.0590289272,54:0.0713188329):0.0124766202):0.0511637916,(51:0.0331397393,((55:1.1457E-6,56:0.0101372642):0.0275291815,(57:0.0168890549,58:0.0191733829):0.0353890974):0.011364169):0.0556829866):0.0448862439):0.255146738):0.0866417028,(((62:0.1809145124,63:0.0784622197):0.1540247306,(60:0.1681588648,(61:0.7866413097,64:0.8811464328):0.2282847367):0.1195642534):0.3958053783,((78:0.1605922227,(80:0.910316308,((76:0.0105355558,77:0.0197412173):0.0111659304,(79:0.0461635719,81:0.0353072343):0.0172663726):0.0705241062):0.0315688345):0.1409390498,((67:0.2418169445,73:1.6717901003):0.1262588503,((75:0.1735549868,(74:1.4683695064,(71:0.1265543721,72:0.1733691316):0.0251118299):0.0563395373):0.1719580231,(66:0.5000380255,(65:0.233248239,(68:0.138861418,(69:0.2029130016,70:0.6404177333):0.0600336936):0.129672863):0.0995379588):0.0939030808):0.0620416928):0.2842711063):0.1489465672):0.1599965519):0.1723388519):0.075439991):0.093277607):0.1928877646):0.1352898437)[% ] [% ] [% setBetweenBits = selected ]; END; BEGIN TREES; Title 'Trees from "DBDLBD_Bayesian.nex"'; LINK Taxa = 'Species_list_nuclear_receptors'; TRANSLATE 1 Homo_sapiens_THRa, 2 Homo_sapiens_THRb, 3 Crassostrea_gigas_NR1A, 4 Crassostrea_gigas_NR1B, 5 Homo_sapiens_RARa, 6 Homo_sapiens_RARb, 7 Homo_sapiens_RARg, 8 Lymnaea_stagnalis_RAR, 9 Homo_sapiens_PPARa, 10 Homo_sapiens_PPARb, 11 Homo_sapiens_PPARg, 12 Crassostrea_gigas_NR1C, 13 Homo_sapiens_Reverba, 14 Homo_sapiens_Reverbb, 15 Mytilus_galloprovincialis_NR1Dv1, 16 Crassostrea_gigas_NR1D, 17 Caenorhabditis_elegans_NHR85, 18 Drosophila_melanogaster_E75, 19 Crassostrea_gigas_NR1CDEFa, 20 Crassostrea_gigas_NR1CDEFb, 21 Mytilus_galloprovincialis_NR1DEF, 22 Crassostrea_gigas_NR1E, 23 Drosophila_melanogaster_E78, 24 Caenorhabditis_elegans_SEX1, 25 Homo_sapiens_RORa, 26 Homo_sapiens_RORb, 27 Homo_sapiens_RORg, 28 Crassostrea_gigas_NR1F, 29 Caenorhabditis_elegans_NHR23, 30 Drosophila_melanogaster_DHR3, 31 Homo_sapiens_LXRb, 32 Homo_sapiens_LXRa, 33 Crassostrea_gigas_NR1H, 34 Drosophila_melanogaster_EcR, 35 Homo_sapiens_FXR, 36 Homo_sapiens_VDR, 37 Homo_sapiens_PXR, 38 Homo_sapiens_CAR, 39 Drosophila_melanogaster_DHR96, 40 Caenorhabditis_elegans_DAF12, 41 Caenorhabditis_elegans_NHR8, 42 Crassostrea_gigas_NR1Ja, 43 Crassostrea_gigas_NR1Jb, 44 Crassostrea_gigas_NR1Jg, 45 Crassostrea_gigas_NR2A, 46 Caenorhabditis_elegans_NHR64, 47 Caenorhabditis_elegans_NHR69, 48 Homo_sapiens_HNF4a, 49 Homo_sapiens_HNF4b, 50 Drosophila_melanogaster_HNF4, 51 Crassostrea_gigas_NR2B, 52 Homo_sapiens_RXRa, 53 Homo_sapiens_RXRb, 54 Homo_sapiens_RXRg, 55 Lymnaea_stagnalis_RXR, 56 Biomphalaria_glabrata_RXR, 57 Thais_clavigera_RXR, 58 Nucella_lapillus_RXR, 59 Drosophila_melanogaster_USP, 60 Crassostrea_gigas_NR2CD, 61 Caenorhabditis_elegans_NHR41, 62 Homo_sapiens_TR2, 63 Homo_sapiens_TR4, 64 Drosophila_melanogaster_DHR78, 65 Homo_sapiens_TLX, 66 Drosophila_melanogaster_DSF, 67 Crassostrea_gigas_NR2E5, 68 Crassostrea_gigas_NR2E1, 69 Crassostrea_gigas_NR2E2, 70 Drosophila_melanogaster_TLL, 71 Drosophila_melanogaster_DHR51, 72 Crassostrea_gigas_NR2E3, 73 Drosophila_melanogaster_DHR83, 74 Caenorhabditis_elegans_FAX1, 75 Homo_sapiens_PNR, 76 Homo_sapiens_COUPTF1, 77 Homo_sapiens_COUPTF2, 78 Homo_sapiens_EAR2, 79 Drosophila_melanogaster_SVP, 80 Caenorhabditis_elegans_UNC55, 81 Crassostrea_gigas_NR2F, 82 Homo_sapiens_ERa, 83 Homo_sapiens_ERb, 84 Mytilus_edulis_ER, 85 Crassostrea_gigas_ER, 86 Octopus_vulgaris_ER, 87 Aplysia_californica_ER, 88 Thais_clavigera_ER, 89 Marisa_cornuarietis_ER, 90 Nucella_lapillus_ER, 91 Crassostrea_gigas_NR3A, 92 Homo_sapiens_ERRa, 93 Homo_sapiens_ERRb, 94 Homo_sapiens_ERRg, 95 Marisa_cornuarietis_ERR, 96 Crassostrea_gigas_NR3B, 97 Drosophila_melanogaster_DERR, 98 Homo_sapiens_GR, 99 Homo_sapiens_MR, 100 Homo_sapiens_PR, 101 Homo_sapiens_AR, 102 Crassostrea_gigas_NR4A, 103 Drosophila_melanogaster_DHR38, 104 Caenorhabditis_elegans_NHR6, 105 Homo_sapiens_NGFIB, 106 Homo_sapiens_NURR1, 107 Homo_sapiens_NOR1, 108 Homo_sapiens_SF1, 109 Homo_sapiens_LRH, 110 Crassostrea_gigas_NR5B, 111 Caenorhabditis_elegans_NHR25, 112 Drosophila_melanogaster_FTZF1, 113 Drosophila_melanogaster_DHR39, 114 Crassostrea_gigas_NR5A, 115 Caenorhabditis_elegans_NHR91, 116 Drosophila_melanogaster_DHR4, 117 Homo_sapiens_GCNF, 118 Crassostrea_gigas_NHR43, 119 Crassostrea_gigas_NR1P7, 120 Crassostrea_gigas_NR1P1, 121 Crassostrea_gigas_NR1P3, 122 Crassostrea_gigas_NR1P8, 123 Crassostrea_gigas_NR1P9, 124 Crassostrea_gigas_NR1P6, 125 Crassostrea_gigas_NR1P4, 126 Crassostrea_gigas_NR1P5, 127 Crassostrea_gigas_NR1P2, 128 Crassostrea_gigas_NR1P10, 129 Mytilus_galloprovincialis_NR1G, 130 Crassostrea_gigas_NR1P11, 131 Crassostrea_gigas_NHR42; TREE con_50_majrule = ((131:0.4896451,((104:0.8171663,((102:0.2024617,103:0.1058784):0.07214758,(105:0.1174368,(106:0.04692854,107:0.1815808):0.03950776):0.04872544):0.1125118):0.2926574,(((3:0.180048,(1:0.062054,2:0.03041627):0.2662631):0.196794,(((31:0.1369681,32:0.07972672):0.2075349,(35:0.3871148,(33:0.3348065,34:0.2820418):0.103282):0.0616777):0.1506446,((36:0.2733013,(37:0.2100505,38:0.3411915):0.1603142):0.1281106,(44:0.4180928,((42:0.3170888,43:0.2542354):0.08005111,(39:0.3140076,(40:0.4571561,41:0.6387102):0.1976368):0.130988):0.1288799):0.3162245):0.1559694):0.1597875):0.0501993,(((4:0.07741426,8:0.104732):0.0773104,(7:0.03311172,(5:0.03948123,6:0.02362129):0.02099845):0.1495734):0.1592006,((128:0.3111735,(129:0.3487938,130:0.3234836):0.1395899,((122:0.5462964,123:0.2076072):0.1796255,(119:0.2145488,((121:0.241825,(120:0.1545289,127:0.4576511):0.1016038):0.1483148,(124:0.4414493,125:0.3000229,126:0.2152447):0.06838858):0.1324946):0.3140337):0.1082752):0.344335,((118:1.343586,(22:0.1386677,23:0.2574099):0.1499079):0.185254,((20:0.4189053,(19:0.3005377,21:0.07748609):0.3830313):0.09686547,((26:0.1108321,(25:0.08591203,27:0.2227608):0.04898097):0.166423,(28:0.1810375,(29:0.5560438,30:0.1988265):0.1021638):0.1528268):0.1416994):0.04042431,((17:0.7286824,24:0.6429186):0.2555774,(12:0.6534926,(11:0.08740627,(9:0.1077915,10:0.09062586):0.07909142):0.3444737):0.1775511,((13:0.08387426,14:0.03995927):0.1879325,(18:0.291823,(15:0.0739991,16:0.0611925):0.04827671):0.09095103):0.04314163):0.06468555):0.1174722):0.1290362):0.03597744):0.1754317):0.1188124):0.03543047,(((97:0.3650436,((95:0.08564023,96:0.06826158):0.1926821,(92:0.1424167,(93:0.0604821,94:0.0440929):0.06308709):0.1356492):0.05705806):0.1549435,(((98:0.1373784,99:0.1443036):0.05007488,(100:0.1178171,101:0.2281872):0.05341629):0.6272509,((82:0.124615,83:0.1720129):0.155458,((88:0.01266234,90:0.01627769):0.01874676,(89:0.02952482,(87:0.09025236,(86:0.1263827,(84:0.06758792,(85:0.002393327,91:0.002423494):0.05413829):0.05952874):0.02149672):0.0421411):0.03497876):0.2600886):0.1489465):0.1646862):0.229358,(((117:0.4906288,(115:0.4466853,116:0.4185395):0.1918502):0.233254,((110:0.3058376,113:0.2757853):0.2337232,(114:0.1929987,((108:0.2171854,109:0.03948158):0.123646,(111:0.8857589,112:0.1646068):0.1290892):0.06117731):0.2254042):0.1376877):0.1157635,((((46:0.3695006,47:0.3307423):0.2318204,((45:0.06231956,50:0.1321997):0.02992711,(48:0.05205788,49:0.04052857):0.07747574):0.1178465):0.2451919,(59:0.2779244,((52:0.00752725,(53:0.04337169,54:0.0532672):0.01206481):0.03607291,(51:0.02424047,((55:0.003440606,56:0.008223148):0.02322086,(57:0.01556062,58:0.01484176):0.02668243):0.0113757):0.04017816):0.04469581):0.1729559):0.06981283,(((62:0.1268542,63:0.06573609):0.1160098,(60:0.1158777,(61:0.4865821,64:0.5305396):0.1890859):0.08404583):0.2639083,((78:0.1065068,(80:0.6111717,((76:0.009705651,77:0.01553039):0.01249001,(79:0.03445508,81:0.02509718):0.01419958):0.04370371):0.0404001):0.09896632,((67:0.1811587,73:0.9932046):0.08468326,((75:0.1268483,(71:0.0897257,72:0.115812,74:0.9326989):0.04472911):0.1157692,(66:0.3315321,(65:0.1515797,(68:0.09926381,(69:0.1475346,70:0.4141215):0.04318992):0.08540313):0.08409205):0.06782753):0.05302138):0.1902449):0.1061486):0.09935671):0.1246209):0.06235468):0.03543047)[% ] [% ] [% setBetweenBits = selected ]; END; BEGIN TREES; Title 'Tree block 3 from "DBDLBD_NJ.nex"'; LINK Taxa = 'Species_list_nuclear_receptors'; TRANSLATE 1 Homo_sapiens_THRa, 2 Homo_sapiens_THRb, 3 Crassostrea_gigas_NR1A, 4 Crassostrea_gigas_NR1B, 5 Homo_sapiens_RARa, 6 Homo_sapiens_RARb, 7 Homo_sapiens_RARg, 8 Lymnaea_stagnalis_RAR, 9 Homo_sapiens_PPARa, 10 Homo_sapiens_PPARb, 11 Homo_sapiens_PPARg, 12 Crassostrea_gigas_NR1C, 13 Homo_sapiens_Reverba, 14 Homo_sapiens_Reverbb, 15 Mytilus_galloprovincialis_NR1Dv1, 16 Crassostrea_gigas_NR1D, 17 Caenorhabditis_elegans_NHR85, 18 Drosophila_melanogaster_E75, 19 Crassostrea_gigas_NR1CDEFa, 20 Crassostrea_gigas_NR1CDEFb, 21 Mytilus_galloprovincialis_NR1DEF, 22 Crassostrea_gigas_NR1E, 23 Drosophila_melanogaster_E78, 24 Caenorhabditis_elegans_SEX1, 25 Homo_sapiens_RORa, 26 Homo_sapiens_RORb, 27 Homo_sapiens_RORg, 28 Crassostrea_gigas_NR1F, 29 Caenorhabditis_elegans_NHR23, 30 Drosophila_melanogaster_DHR3, 31 Homo_sapiens_LXRb, 32 Homo_sapiens_LXRa, 33 Crassostrea_gigas_NR1H, 34 Drosophila_melanogaster_EcR, 35 Homo_sapiens_FXR, 36 Homo_sapiens_VDR, 37 Homo_sapiens_PXR, 38 Homo_sapiens_CAR, 39 Drosophila_melanogaster_DHR96, 40 Caenorhabditis_elegans_DAF12, 41 Caenorhabditis_elegans_NHR8, 42 Crassostrea_gigas_NR1Ja, 43 Crassostrea_gigas_NR1Jb, 44 Crassostrea_gigas_NR1Jg, 45 Crassostrea_gigas_NR2A, 46 Caenorhabditis_elegans_NHR64, 47 Caenorhabditis_elegans_NHR69, 48 Homo_sapiens_HNF4a, 49 Homo_sapiens_HNF4b, 50 Drosophila_melanogaster_HNF4, 51 Crassostrea_gigas_NR2B, 52 Homo_sapiens_RXRa, 53 Homo_sapiens_RXRb, 54 Homo_sapiens_RXRg, 55 Lymnaea_stagnalis_RXR, 56 Biomphalaria_glabrata_RXR, 57 Thais_clavigera_RXR, 58 Nucella_lapillus_RXR, 59 Drosophila_melanogaster_USP, 60 Crassostrea_gigas_NR2CD, 61 Caenorhabditis_elegans_NHR41, 62 Homo_sapiens_TR2, 63 Homo_sapiens_TR4, 64 Drosophila_melanogaster_DHR78, 65 Homo_sapiens_TLX, 66 Drosophila_melanogaster_DSF, 67 Crassostrea_gigas_NR2E5, 68 Crassostrea_gigas_NR2E1, 69 Crassostrea_gigas_NR2E2, 70 Drosophila_melanogaster_TLL, 71 Drosophila_melanogaster_DHR51, 72 Crassostrea_gigas_NR2E3, 73 Drosophila_melanogaster_DHR83, 74 Caenorhabditis_elegans_FAX1, 75 Homo_sapiens_PNR, 76 Homo_sapiens_COUPTF1, 77 Homo_sapiens_COUPTF2, 78 Homo_sapiens_EAR2, 79 Drosophila_melanogaster_SVP, 80 Caenorhabditis_elegans_UNC55, 81 Crassostrea_gigas_NR2F, 82 Homo_sapiens_ERa, 83 Homo_sapiens_ERb, 84 Mytilus_edulis_ER, 85 Crassostrea_gigas_ER, 86 Octopus_vulgaris_ER, 87 Aplysia_californica_ER, 88 Thais_clavigera_ER, 89 Marisa_cornuarietis_ER, 90 Nucella_lapillus_ER, 91 Crassostrea_gigas_NR3A, 92 Homo_sapiens_ERRa, 93 Homo_sapiens_ERRb, 94 Homo_sapiens_ERRg, 95 Marisa_cornuarietis_ERR, 96 Crassostrea_gigas_NR3B, 97 Drosophila_melanogaster_DERR, 98 Homo_sapiens_GR, 99 Homo_sapiens_MR, 100 Homo_sapiens_PR, 101 Homo_sapiens_AR, 102 Crassostrea_gigas_NR4A, 103 Drosophila_melanogaster_DHR38, 104 Caenorhabditis_elegans_NHR6, 105 Homo_sapiens_NGFIB, 106 Homo_sapiens_NURR1, 107 Homo_sapiens_NOR1, 108 Homo_sapiens_SF1, 109 Homo_sapiens_LRH, 110 Crassostrea_gigas_NR5B, 111 Caenorhabditis_elegans_NHR25, 112 Drosophila_melanogaster_FTZF1, 113 Drosophila_melanogaster_DHR39, 114 Crassostrea_gigas_NR5A, 115 Caenorhabditis_elegans_NHR91, 116 Drosophila_melanogaster_DHR4, 117 Homo_sapiens_GCNF, 118 Crassostrea_gigas_NHR43, 119 Crassostrea_gigas_NR1P7, 120 Crassostrea_gigas_NR1P1, 121 Crassostrea_gigas_NR1P3, 122 Crassostrea_gigas_NR1P8, 123 Crassostrea_gigas_NR1P9, 124 Crassostrea_gigas_NR1P6, 125 Crassostrea_gigas_NR1P4, 126 Crassostrea_gigas_NR1P5, 127 Crassostrea_gigas_NR1P2, 128 Crassostrea_gigas_NR1P10, 129 Mytilus_galloprovincialis_NR1G, 130 Crassostrea_gigas_NR1P11, 131 Crassostrea_gigas_NHR42; TREE tree_1 = (((((3:0.23056,(1:0.05135,2:0.06312):0.20658):0.14358,((4:0.10141,8:0.12065):0.07356,(7:0.04895,(5:0.04597,6:0.03135):0.0108):0.15594):0.1395):0.04849,(((31:0.12486,32:0.13549):0.21299,(35:0.33856,(33:0.31201,34:0.27086):0.06868):0.01304):0.09017,((36:0.33565,(37:0.27715,38:0.30572):0.0566):0.10741,((41:0.49098,(39:0.40723,40:0.46683):0.03881):0.05763,(44:0.40238,(42:0.31227,43:0.30359):0.05474):0.04968):0.14836):0.05553):0.0478):0.01298,((118:0.74967,(((122:0.42813,123:0.38077):0.09806,(128:0.35523,(129:0.36171,130:0.34301):0.03964):0.06334):0.01292,(127:0.41063,((120:0.24726,121:0.27025):0.10601,(119:0.29934,(124:0.38329,(125:0.29937,126:0.28865):0.03781):0.01783):0.02069):0.0604):0.10748):0.13355):0.01081,((12:0.52419,(11:0.13899,(9:0.14153,10:0.1073):0.04218):0.23967):0.06439,((17:0.55633,24:0.53872):0.07863,(((27:0.18933,(25:0.13816,26:0.14193):0.06082):0.12667,(29:0.38418,(28:0.2373,30:0.28363):0.04799):0.05815):0.09022,((20:0.36639,(19:0.19523,21:0.19335):0.29853):0.06806,((22:0.19626,23:0.2585):0.13283,((13:0.07578,14:0.08485):0.17121,(18:0.27355,(15:0.08997,16:0.0824):0.10383):0.04433):0.05662):0.01432):0.01682):0.00858):0.02062):0.04475):0.03264):0.031985,((104:0.59342,((102:0.19752,103:0.14437):0.05155,(105:0.12329,(106:0.12927,107:0.13914):0.04329):0.03046):0.14162):0.15195,(131:0.48484,((((117:0.45607,(115:0.35569,116:0.43814):0.0884):0.07453,((110:0.34111,113:0.32261):0.12019,(111:0.54699,(114:0.22064,(112:0.30998,(108:0.17889,109:0.12817):0.04701):0.03539):0.10196):0.04715):0.10647):0.02703,((101:0.24002,(99:0.15137,(98:0.16258,100:0.18643):0.00976):0.04339):0.36924,((97:0.31422,((95:0.10094,96:0.09035):0.16688,(92:0.14921,(93:0.06337,94:0.06923):0.07782):0.09021):0.01794):0.09166,((82:0.17278,83:0.18341):0.11263,(86:0.1326,((84:0.08292,(85:0.0,91:0.0):0.07273):0.04423,(87:0.12973,(89:0.05941,(88:0.01921,90:0.01609):0.03318):0.01585):0.02107):0.02008):0.19081):0.13575):0.05315):0.0683):0.01781,((((46:0.38254,47:0.30167):0.08179,((45:0.11543,50:0.11792):0.01453,(48:0.0482,49:0.06132):0.06132):0.18788):0.12202,(59:0.23228,((54:0.04929,(52:0.02697,53:0.04463):0.01299):0.02898,((57:0.00902,58:0.02611):0.02381,(51:0.03418,(55:0.00496,56:0.00494):0.02454):0.00903):0.03967):0.1119):0.1416):0.0595,(((61:0.44373,64:0.43933):0.04179,(60:0.20747,(62:0.12497,63:0.11204):0.10815):0.13502):0.06483,((80:0.46313,(78:0.12763,((76:0.01744,77:0.01274):0.01939,(79:0.0374,81:0.03992):0.00778):0.08066):0.14094):0.05317,((73:0.57143,74:0.59527):0.05094,(67:0.27159,((70:0.35243,(65:0.18164,(68:0.13997,69:0.19789):0.06674):0.06675):0.03927,(66:0.29565,(75:0.15199,(71:0.10395,72:0.14848):0.05329):0.07609):0.04119):0.01884):0.06756):0.04594):0.05623):0.02303):0.04734):0.00939):0.03512):0.031985)[% ] [% ] [% setBetweenBits = selected ]; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 221; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 221; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1396454669329; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 5169790375168251633; tell It; attachments ; endTell; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 4737874868531960516; mqVersion 275; checksumv 0 3 4003832916 null getNumChars 221 numChars 221 getNumTaxa 131 numTaxa 131 short false bits 1048575 states 1048575 sumSquaresStatesOnly 2.6964434012144E14 sumSquares 2.6964434012144E14 longCompressibleToShort false usingShortMatrix false NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 355; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1920 944; setLocation -9 -9; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #5169790375168251633 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #5169790375168251633; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1565 877; setLocation -9 -9; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; endTell; showWindow; getEmployee #mesquite.lists.ColorTaxon.ColorTaxon; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.lists.TaxonListAnnotPanel.TaxonListAnnotPanel; tell It; togglePanel off; endTell; endTell; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #5169790375168251633 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 833.1396452631828.1642400398410813024; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1565 877; setLocation -9 -9; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.reroot; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; endTell; setEdgeWidth 6; orientUp; setCornerMode Right_Angle 50; endTell; setBackground White; setBranchColor Black; showNodeNumbers off; showBranchColors on; labelBranchLengths off; centerBrLenLabels on; showBrLensUnspecified on; showBrLenLabelsOnTerminals on; setBrLenLabelColor 0 0 255; setNumBrLenDecimals 6; desuppress; getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames; tell It; setColor Black; toggleColorPartition on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; showWindow; endTell; desuppressEPCResponse; getEmployee #mesquite.trees.ColorBranches.ColorBranches; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.ornamental.BranchNotes.BranchNotes; tell It; setAlwaysOn off; endTell; getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition; tell It; colorByPartition off; endTell; getEmployee #mesquite.ornamental.DrawTreeAssocDoubles.DrawTreeAssocDoubles; tell It; setOn on; setDigits 4; writeAsPercentage off; toggleCentred on; toggleHorizontal on; toggleWhiteEdges on; setFontSize 10; setOffset 0 0; endTell; getEmployee #mesquite.ornamental.DrawTreeAssocStrings.DrawTreeAssocStrings; tell It; setOn on; toggleCentred on; toggleHorizontal on; setFontSize 10; setOffset 0 0; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; makeTreeWindow #5169790375168251633 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 3; toggleUseWeights off; endTell; setAssignedID 863.1396452647399.5901455196073006839; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1565 877; setLocation -9 -9; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.reroot; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; endTell; setEdgeWidth 6; orientUp; setCornerMode Right_Angle 50; endTell; setBackground White; setBranchColor Black; showNodeNumbers off; showBranchColors on; labelBranchLengths off; centerBrLenLabels on; showBrLensUnspecified on; showBrLenLabelsOnTerminals on; setBrLenLabelColor 0 0 255; setNumBrLenDecimals 6; desuppress; getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames; tell It; setColor Black; toggleColorPartition on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; showWindow; endTell; desuppressEPCResponse; getEmployee #mesquite.trees.ColorBranches.ColorBranches; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.ornamental.BranchNotes.BranchNotes; tell It; setAlwaysOn off; endTell; getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition; tell It; colorByPartition off; endTell; getEmployee #mesquite.ornamental.DrawTreeAssocDoubles.DrawTreeAssocDoubles; tell It; setOn on; setDigits 4; writeAsPercentage off; toggleCentred on; toggleHorizontal on; toggleWhiteEdges on; setFontSize 10; setOffset 0 0; endTell; getEmployee #mesquite.ornamental.DrawTreeAssocStrings.DrawTreeAssocStrings; tell It; setOn on; toggleCentred on; toggleHorizontal on; setFontSize 10; setOffset 0 0; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; makeTreeWindow #5169790375168251633 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 2; toggleUseWeights off; endTell; setAssignedID 893.1396452648599.876060755614351718; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1565 877; setLocation -9 -9; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.reroot; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; endTell; setEdgeWidth 6; orientUp; setCornerMode Right_Angle 50; endTell; setBackground White; setBranchColor Black; showNodeNumbers off; showBranchColors on; labelBranchLengths off; centerBrLenLabels on; showBrLensUnspecified on; showBrLenLabelsOnTerminals on; setBrLenLabelColor 0 0 255; setNumBrLenDecimals 6; desuppress; getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames; tell It; setColor Black; toggleColorPartition on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; showWindow; endTell; desuppressEPCResponse; getEmployee #mesquite.trees.ColorBranches.ColorBranches; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.ornamental.BranchNotes.BranchNotes; tell It; setAlwaysOn off; endTell; getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition; tell It; colorByPartition off; endTell; getEmployee #mesquite.ornamental.DrawTreeAssocDoubles.DrawTreeAssocDoubles; tell It; setOn on; setDigits 4; writeAsPercentage off; toggleCentred on; toggleHorizontal on; toggleWhiteEdges on; setFontSize 10; setOffset 0 0; endTell; getEmployee #mesquite.ornamental.DrawTreeAssocStrings.DrawTreeAssocStrings; tell It; setOn on; toggleCentred on; toggleHorizontal on; setFontSize 10; setOffset 0 0; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #4737874868531960516 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1565 877; setLocation -9 -9; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; colorCells #mesquite.charMatrices.ColorByState.ColorByState; tell It; setStateLimit 9; toggleUniformMaximum on; endTell; colorRowNames #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor; colorColumnNames #mesquite.charMatrices.CharGroupColor.CharGroupColor; colorText #mesquite.charMatrices.NoColor.NoColor; setBackground White; toggleShowNames on; toggleShowTaxonNames on; toggleTight off; toggleThinRows off; toggleShowChanges off; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames off; toggleAutoTaxonNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleShowPaleGrid off; toggleShowPaleCellColors off; togglePaleInapplicable on; toggleShowBoldCellText off; toggleAllowAutosize off; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; showWindow; getWindow; tell It; forceAutosize; endTell; getEmployee #mesquite.charMatrices.ColorCells.ColorCells; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel; tell It; togglePanel off; endTell; getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector; tell It; autotabOff; endTell; getEmployee #mesquite.charMatrices.SelSummaryStrip.SelSummaryStrip; tell It; showStrip off; endTell; getEmployee #mesquite.align.AlignToDropped.AlignToDropped; tell It; gapCosts 8 3 2 2; subCosts 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5; endTell; getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; endTell; endTell; endTell; end;