#NEXUS [!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file. Generated on September 19, 2025; 16:54 GMT TreeBASE (cc) 1994-2008 Study reference: Belahbib H., Renard E., Santini S., Jourda C., Clavery J., Borchiellini C., & Le bivic A. 2018. New Genomic Data and Analyses Challenge the Traditional Vision of Epithelium Evolution in Sponges and Ctenophores. BMC Genomics, . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S22408] [ The following blocks are input data for analysis step 22821 ] BEGIN TAXA; TITLE TaxaForAnalysisStep22821; DIMENSIONS NTAX=31; TAXLABELS 'A.queenslandica_vinc' 'A.vastus_Acat' 'A.vastus_vinc' 'A_queenslandica_Acat' 'B.floridae_Acat' 'B.floridae_vinc-a' 'B.floridae_vinc-b' 'D.melanogaster_vinc' 'D_melanogaster_Acat' 'L.complicata_Acat' 'L.complicata_vinc-a' 'L.complicata_vinc-b' 'M.leidyi_Acat' 'M.leidyi_vinc' 'M.musculus_Acat' 'M.musculus_vinc' 'N.vectensis_Acat' 'N_vectensis_vinc' 'O.carmela_Acat' 'O.carmela_vinc' 'O.lobularis_Acat' 'O.lobularis_vinc' 'O.minuta_Acat' 'O.minuta_vinc' 'P.ficiformis_Acat' 'P.ficiformis_vinc' 'S.ciliatum_Acat' 'S.ciliatum_vinc-a' 'S.ciliatum_vinc-b' 'T.adhaerens_Acat' 'T.adhaerens_vinc' ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M45606] TITLE Character_Matrix_figure_S1C; LINK TAXA = TaxaForAnalysisStep22821; DIMENSIONS NCHAR=229; FORMAT DATATYPE=Protein SYMBOLS= "A C D E F G H I K L M N P Q R S T V W Y" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 ] [ . . . . . . . . . . . . . . . . . . . . . . ] 'A.queenslandica_vinc' SDLVQPVTAVKAAVDNLVEVGRQTLKSAKDEKVHTDMPPTFEAIESACTLLLQ-AAKGLSQE-EQTPTDKKK---LLDGSRGILQGVSHLLLVYDQYEVRKIIKTCEGVIDYIKVAEIV-----QSMEELLQFTKNLSPAITNMTKQVDGRREDL----TNASHAAILEDESEQVKKGLPLLLSAMKAFVTIKRDG-RKGAEDAQENRNYIVGAITDSIREIIRVLQL- 'A.vastus_Acat' ------------------------------------MLSAVHRLKGSARQLRERVVGSSLLN-SCENENPGQDVTVREVSRALLYDVASVLSVADKLDGKRLVETSLSVENCLEKLKHA-----LSLQELYQHIRQFTPVMAGLTKLARQRQEELACCEENSCLVESLSWYRRELAMGCALLIPSCKCYVK------HPDLQTSRSTRDFALEVILDAANYISRIAKE- 'A.vastus_vinc' -NIGLHLKEVTAAVENLLQVGQNLSETSKDELLKKELPVAGEKIEQSCLLVNK-AAKAFEPGAQGEVEDKHL---MLDGARGILSGVSMLLLVWDESEIRKVLDICDRIVEYLSVVEQV-----ETHEEVATVSSNLQPGMNSLVNHVRARADDL----IDKTLQGMLNEEVQNTERYQSVLMSCMQMYVSVRGSQGPQGLLDAQRGRNAAQRTLVDSINELKRILQL- 'A_queenslandica_Acat' ----------------------------------------------------------------------------------------------------------------------------------------------------------MK----GNAAQQLLVAAHTELKQCNKILITSTKIFLE------HPEDPHAQENRDYVIQRMQEAVKTISMLADG- 'B.floridae_Acat' KKAHVLSALVKKATETFIDKGEIIAKD--YPDIQDDMMAAIDDCKKTGDTMYA-ASQEFADD-PCSSMKRGA---MVRAARALLSAVTRLLIIADMADVHMLLKHLRIVEESLERVRQA-----QDQQALNNAFRQYGKDVVGLNDIAMKRQNDL----IDPARRDEMAAARNTLKKNSMMLYTASKAFLR------HPDVAAAKANRDYVYKQVCDAVNSLSNTAQA- 'B.floridae_vinc-a' PDLARPVQAVCAAVQNLVKVAKETAETSQDVILKQEMPIAYTRVEEASHLLVD-ASDMLRAD-PYSRPAREK---LIDGARGILSGTSQLLLTFDEAEVRKIIRVCKSVLEYLAIAEVV-----ETMEDLVTFVKNLTPGMTGMSKMVDARSKEL----THQQHRESLAHSLQVVKDLTPVLISGIKIFVTTRRPQ-GLGIPEAIENRNYVVNKMSAEISEIIRVLQL- 'B.floridae_vinc-b' PDLARPVQAVCAAVQNLVKVAKETAETSQDVILKQEMPIAYTRVEEASHLLVD-ASDMLRAD-PYSRPAREK---LIDGARGILSGTSQLLLTFDEAEVRKIIRVCKSVLEYLAIAEVV-----ETMEDLVTFVKNLTPGMTGMSKMVDARSKEL----THQQHRESLAHSLQVVKDLTPVLISGIKIFVTTRRPQDGKGIPEAIENRNYVVNKMSAEISEIIRVLQL- 'D.melanogaster_vinc' PDLSRPVQVVSAAVANLVKVGRDTINSSDDKILRQDMPSALHRVEGASQLLEE-ASDMLRSD-PYSGPARKK---LIEGSRGILQGTSSLLLCFDESEVRKIIQECKRVLDYLAVAEVI-----NTMEQLVQFLKDLSPCLSKVHREVGAREKEL----THQVHSEILVRCLEQVKTLAPILICSMKVYIHIVEQQ-GRGAEEAAENRNYLAARMSDELQEIIRVLQL- 'D_melanogaster_Acat' KRASALVAAVEKATENFIQKGEQIAYE--NPDITQEMLTAVDEVKKTGDAMSI-AAREFSED-PCSSLKRGN---MVRAARNLLSAVTRLLILADMVDVHLLLKSLHIVEDDLNKLKNA-----SSQDELMDNMRQFGRNAGELIKQAAKRQQEL----KDPQLRDDLAAARAMLKKHSTMLLTASKVYVR------HPELDLAKVNRDFILKQVCDAVNTISDVAQG- 'L.complicata_Acat' QRIQTVLADLQRKAALIERNDDLGITAAVRHRIIMDYDSAVEHADDIVAQLTQ-STTGAADILAVDKIGRS--------AQGILSSVTSALFAFDQTVIIRIEAIAAKISENGTSLTRILEASPVHVDSLQDSLKQLSDHMVKLSEITRGRIQDL----KDGCQRNEMDCCRVMLEHCFRSFLSAVKVRLQ------HSVLSIGRMNCMAVMDNFLEVVGTITRAAAL- 'L.complicata_vinc-a' PDLSEPVSAVSAAVGTLVKVGKETAESSNDEQLQQDLPRAWESAELASQQLTE-AAQTLRDN-PRSAPGRRL---LISGARGILEAVSDLLLTFDEAEVRRIIMVCESVKEYLSVADVI-----EIMDDLVTFIKNLTPGATGLNKLIDNRAKEL----TNPVHAAKLVEHCDHVKKSIPMLISSIKLVCSLKASR-SGDVSEAASSRNWLVGTMNEDLDEIIRILKI- 'L.complicata_vinc-b' PDLTPQVDVVAAAVMTLVKVGEQTADDSDDQILKKELPRSLKSVEKASSQLVE-ASQTLKEN-GKSMPGRRL---LIVGARGILQGISDLLITNDESEVRTMVVACRDSQVVLRDAAGV-----RGMPNLVEFVKRLTPSLTETSKHVDRRQKEL----TNASHAAELVEHCDHLRKFVPMLISSIKLVSHLEHRG-AASTKDAVENRDYVTRAMNEHIEEIIRILQL- 'M.leidyi_Acat' RKLLQHAKHINEICYELIKFAREVAKE--HPDVEYELNQACNRTCDVYNVMKMKIEGDDKHD------SAGT---IIDIAKQLINNVARILIVTDSADLILINKTIEDVKQCLKAVEQC-----IEFCALDEIFQKLRSVMDTLMKQIASRQMDL----LDTQKKDELGLVRSMWMRCKERLYTSSRVAIV------HPELESGVTNRNLVLQEINESIKKLQAIIKG- 'M.leidyi_vinc' PDLVDNIKLVLTCVSNLATVAESTAQQSNDATFIRDFPSAMDAVNSSSAALNE-AVLELRTD-PYSSQGRRK---LITGAKGILTGTCDLLLMYDESEVRKIVKNCEAVKSYFPVCLEV-----GTLEDLSFYIKNLTPGLTQVCKAVQNRAQEL----LHKPYADILRRETEQLKKFAPMLIGASKSLINAQN---EELTNAAHQNLDNTIEKMNASMKEIIRVLLM- 'M.musculus_Acat' KKAHVLAASVEQATENFLEKGDKIAKE--SQFLKEELVVAVEDVRKQGDLMKS-AAGEFADD-PCSSVKRGN---MVRAARALLSAVTRLLILADMADVYKLLVQLKVVEDGILKLRNA-----GNEQDLGIQYKALKPEVDKLNIMAAKRQQEL----KDVGNRDQMAAARGILQKNVPILYTASQACLQ------HPDVAAYKANRDLIYKQLQQAVTGISNAAQA- 'M.musculus_vinc' PDLTAPVAAVQAAVSNLVRVGKETVQTTEDQILKRDMPPAFIKVENACTKLVQ-AAQMLQSD-PYSVPARDY---LIDGSRGILSGTSDLLLTFDEAEVRKIIRVCKGILEYLTVAEVV-----ETMEDLVTYTKNLGPGMTKMAKMIDERQQEL----THQEHRVMLVNSMNTVKELLPVLISAMKIFVTTKNSK-NQGIEEALKNRNFTVEKMSAEINEIIRVLQL- 'N.vectensis_Acat' KNAHKLAQDIEDATVRLIKTGESISKD--FPEIREEMIAACKDCRGAGDTMHI-SSKEFADD-PCTSTKRMT---MVRAARALLSSVTRLLCVADMADVCRLLASLKLVERRLKDLEGA-----SNTADLLNSFKNLGNDLMNLAQLSGRRQADL----KDPLRRDEMAAARAILKDASKMLLSSSKAYVR------HPEVASAKANRDFIISQMNEAVNSISGTAQA- 'N_vectensis_vinc' PDLSNPIMAVGAAVANLVKVGKETATQSKDKILKQEMPLAFTRVEESSMLLVQ-ASKLLKRD-PYSSEARQK---LIDGARGILSGTSALLLTFDEAEVRKIVTFCRSLLEYLPVGEMV-----EEMQDLLTFVANLSPAIQNVAKAVESRAAEL----THTVHRDMLKSSLSKLSGMVPLLISSMKAFVKTPP---GAGRPEAQESRNFIINKMSAEITEIIRVLQL- 'O.carmela_Acat' YRSATLVDSLDKARKCFVAEGRKIAQL--NREVEREMLIACEGVESAGLATRD-AAEHFMLD-PCSSEKRSE---LVEVAKELLTSVARLLLIADTADVNHLKSAARSVNTWLYKLERA-----ISPEEVVQLYQGYAIDLENLLKLTTRRQMDV----KSRWVSEKLAFAKVKLRRMGDILSRSVKLHVQ------YPDIASAKVNRDFTLSEATQAVRSITECLDE- 'O.carmela_vinc' EDLTPLVQGVGIAVTNLVQVAASMVETSNDEDFKAELPPSMQEVQQAAVFLSD-AARLLKAD-QGSPEGKRK---LLDGARGVINGMSDLLMCADRSEVRKMVKVCRSVQEYLDVAKVI-----DVEADLATFLQNLTPGMTSMMKVVEQRHPEL----TNLAHAQMLKSELGTVREQIPILISSIRVCCLVIVKDGSSGMKDAAFGRDYVIQKLFIAIEEIIRVLQL- 'O.lobularis_Acat' YSLQPFIDQV--ALARFVAEGRKIGRE--NREIEIDMRSACDRVESTGKEMHA-TARDFLDN-PCSSARRNE---LVESARELLTAVTDLLIIADAADVIRLKSAARQVDNWLQQMERA-----ASPDEVTYLYRGYGNDLEKLLKLTARRQTDV----KSPSISEKLALARLKLKRINNVLLNSMTLHVK------YPDVASAKVNRDFALSQASEAVRSIVESLDE- 'O.lobularis_vinc' QDLTPLVKGVGLAVSNLVEVATGMVSTTNDEEFKVELPPSVEMVKQASTDLDD-AARLLKAD-QGSREGKRK---LLDGARGVINGMSDLLVCADRSEVRKMIKTCRNVQEYLDVAKVI-----DVEADLATFLQNLTPGMTSMMKVVESRHPEL----TNLRHALMLKDELRTVREQIPILISSIKVYCLVFAKKGATGLKEAGFGRDHVITKLYVSIEEIIRVLQL- 'O.minuta_Acat' ISVSLLLQSLDQAVSSLVHTAEIIAYE-NDKKVRRKMLNAVNRLKTSAKQLSQLMSDNIPPS-PTHCIDTEKSPSLRDVARVLLYDVACVLSVADKVDERKLQEATQSIESCLDSLRDV-----VSLTELYQQITQFTPVMARLAKLAKQRQNELDCCEDNSCLVESLSWHRRVLTIGCAMLISSCKCYVR------HPDIETARINRDFSFDVILESSNIIARIMGD- 'O.minuta_vinc' -NIGLHLKEVTAAVENLLQVGQNLSATSKDEILKKELPSAGDKIEQSCTLVNQ-AARAFEPGSQGNIEDKHL---MLDGARGILSGVSTLLLVWDESEIRKVLGICARIIEYLSVVEQV-----ETYEEVATVSSNLQPGMNSLVNHVRARADDL----IEKNLEDMLNSEVRNTEKYHSVLISSMQMYVSVRSSPKLEGLLDAQRGRNCTQGMLVGSIQEIKRIILL- 'P.ficiformis_Acat' RNIYKLIQIVDKATENFNAVAENIATE--NPEFQEELWLSIEEVHTAGNLLHE-AAFDYTSD-VLAPRKREG---MEQAAAGLLKAVTRLLVLIDLIDINELFKASNRVDVKLRQIRDV-----NNWDDFVHSMKVVAKEIQHVSEMAIARQKEL----KNSTAKQLLVAAYVDLTQYNRMLITSTKAFLQ------HPEDESAIENRDYIITRMSEVLKTIAQLADG- 'P.ficiformis_vinc' -----------------------------------------------------------------------------------------------------MVKMCEGIIEYIKVSEMV-----ESIEDVITFTENLAPNLTSMVKLVDTRREEL----TNASHSAILEDELNQVRKGLPLLLSALKTLVGLKKTK-SEGILDAQENRDFIVGSLTESIIEIIRVLQL- 'S.ciliatum_Acat' QHILSVLSKLQRAVPQIPVDNDVGLTAGVRHRIGINYDSAMEHAEELVTCLRQPGPGTAGNSIAVDPAARA--------SQALLTSVTCALYEYDQTIVNRIEMSGQQIARLGEELSSLLMTSTVPSDRLQDVLKSLSETVVVFAQLTEARCKDL----KDPCQKSDMEASRITMEHCFRTLMSSIKVMLQ------HTSLSICRMNCLAVNDNFMDTAALMK--LAA- 'S.ciliatum_vinc-a' PDLSEPVSAVSAAVGKLVTVGKETAESSEDKQLQQDLPRAWEAAEVSSTQLAE-AAATLRDN-PRSGPGRRL---LISGARGILEAVSDLLLTFDESEVRRIISVCESVQEYVKVADVI-----EIMSDLVIFIKNLTPGLTGLNKLIDNRAKEL----TNPVHAAKLVEHCSNVKKAVPMLIASVKLVCSLRASQ-SGDATDAASSRSWLMSTINEDLNEIIRILQI- 'S.ciliatum_vinc-b' PDLTPQVDVVAAAVTTLVTVGEQTADDSEDPILKKELPRPLKSVQKSADQLVE-AAQTLKEN-PVSLPGRRL---LIVGARGILQGISDLLITNDESEVRTMVAACRGSQTVLRDAHIV-----RGIPNLIEFIKGLTPSLTETSKHVDRRQKEL----TNATHAAELVDHCDHLRKFVPMLISSIKLVSHLEARG-GARSREANDNRDFVVKSMNEHIEEIIRILQL- 'T.adhaerens_Acat' KEADDLIKLVHLAINELIEHGQIVAND--NPKIADRVYQAYEELHDAGSCLLA-ATESFVHE-PSSQIKRSA---LLKAVFNLYPILNKLLSIADMVDISNLVKMLHELEDHLQLVLDS-----RDENSLDQNLDNFAYHLDQVDDAVKRRQFDL----KDEDKKDQLSAARANLLTASQLLNVVSKTHFK------YENLPPAKANCAAITSEIREFVNRIVTIIQS- 'T.adhaerens_vinc' PDITMPVQAACAAVANLVQVGQDTANASSDEKFKQEMNVALEVVKNSSVNLNQ-AAHLLKDG-SSSLEARNI---LIDGTKGILSGTSDLLFSYDESEVKKIVRVCNNVKDYMPNASVI-----THEADYQTYTKSVKSAVDNLLIRIRARADDL----LIELNRQLLKRSCINIEDAVTSIESVLKAIIDD-----NQEAEPLQNSRDSFVGIVCEELEEIIRVLML- ; END; [ The following blocks are output data for analysis step 22821 ] BEGIN TREES; TITLE heuristic_tree_alignment_fig_S1C; LINK TAXA = TaxaForAnalysisStep22821; TREE 'Tree 13 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('O.minuta_Acat','A.vastus_Acat'),((((((('D.melanogaster_vinc','M.musculus_vinc'),('B.floridae_vinc-b','B.floridae_vinc-a')),'N_vectensis_vinc'),(((('A.queenslandica_vinc','P.ficiformis_vinc'),('O.lobularis_vinc','O.carmela_vinc')),(('S.ciliatum_vinc-b','L.complicata_vinc-b'),('L.complicata_vinc-a','S.ciliatum_vinc-a'))),'M.leidyi_vinc')),'T.adhaerens_vinc'),('A.vastus_vinc','O.minuta_vinc')),('L.complicata_Acat','S.ciliatum_Acat'))),('O.lobularis_Acat','O.carmela_Acat')),('P.ficiformis_Acat','A_queenslandica_Acat')),(('N.vectensis_Acat',(('M.musculus_Acat','B.floridae_Acat'),'D_melanogaster_Acat')),('M.leidyi_Acat','T.adhaerens_Acat'))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111201] END; BEGIN TREES; TITLE heuristic_tree_alignment_fig_S1C; LINK TAXA = TaxaForAnalysisStep22821; TREE 'Tree 11 from search (criterion: minimize Tree value using character matrix)' = [&R] ((('M.musculus_Acat','B.floridae_Acat'),'D_melanogaster_Acat'),('N.vectensis_Acat',((((('O.minuta_Acat','A.vastus_Acat'),((((((('D.melanogaster_vinc','M.musculus_vinc'),('B.floridae_vinc-b','B.floridae_vinc-a')),'N_vectensis_vinc'),(((('O.lobularis_vinc','O.carmela_vinc'),(('S.ciliatum_vinc-b','L.complicata_vinc-b'),('L.complicata_vinc-a','S.ciliatum_vinc-a'))),('A.queenslandica_vinc','P.ficiformis_vinc')),'M.leidyi_vinc')),'T.adhaerens_vinc'),('A.vastus_vinc','O.minuta_vinc')),('L.complicata_Acat','S.ciliatum_Acat'))),('O.lobularis_Acat','O.carmela_Acat')),('P.ficiformis_Acat','A_queenslandica_Acat')),('M.leidyi_Acat','T.adhaerens_Acat')))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111199] END; BEGIN TREES; TITLE heuristic_tree_alignment_fig_S1C; LINK TAXA = TaxaForAnalysisStep22821; TREE 'Tree 22 from search (criterion: minimize Tree value using character matrix)' = [&R] (('D_melanogaster_Acat',('N.vectensis_Acat',((((('O.minuta_Acat','A.vastus_Acat'),((((((('M.musculus_vinc',('B.floridae_vinc-b','B.floridae_vinc-a')),'D.melanogaster_vinc'),'N_vectensis_vinc'),(((('A.queenslandica_vinc','P.ficiformis_vinc'),('O.lobularis_vinc','O.carmela_vinc')),(('S.ciliatum_vinc-b','L.complicata_vinc-b'),('L.complicata_vinc-a','S.ciliatum_vinc-a'))),'M.leidyi_vinc')),'T.adhaerens_vinc'),('A.vastus_vinc','O.minuta_vinc')),('L.complicata_Acat','S.ciliatum_Acat'))),('O.lobularis_Acat','O.carmela_Acat')),('P.ficiformis_Acat','A_queenslandica_Acat')),('M.leidyi_Acat','T.adhaerens_Acat')))),('M.musculus_Acat','B.floridae_Acat')); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111210] END; BEGIN TREES; TITLE heuristic_tree_alignment_fig_S1C; LINK TAXA = TaxaForAnalysisStep22821; TREE 'Tree 16 from search (criterion: minimize Tree value using character matrix)' = [&R] (('N.vectensis_Acat',(('M.musculus_Acat','B.floridae_Acat'),'D_melanogaster_Acat')),((((('O.minuta_Acat','A.vastus_Acat'),((((((('D.melanogaster_vinc','M.musculus_vinc'),('B.floridae_vinc-b','B.floridae_vinc-a')),'N_vectensis_vinc'),(((('O.lobularis_vinc','O.carmela_vinc'),(('S.ciliatum_vinc-b','L.complicata_vinc-b'),('L.complicata_vinc-a','S.ciliatum_vinc-a'))),('A.queenslandica_vinc','P.ficiformis_vinc')),'M.leidyi_vinc')),'T.adhaerens_vinc'),('A.vastus_vinc','O.minuta_vinc')),('L.complicata_Acat','S.ciliatum_Acat'))),('O.lobularis_Acat','O.carmela_Acat')),('P.ficiformis_Acat','A_queenslandica_Acat')),('M.leidyi_Acat','T.adhaerens_Acat'))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111204] END; BEGIN TREES; TITLE heuristic_tree_alignment_fig_S1C; LINK TAXA = TaxaForAnalysisStep22821; TREE 'Tree 26 from search (criterion: minimize Tree value using character matrix)' = [&R] ('D_melanogaster_Acat',(('M.musculus_Acat','B.floridae_Acat'),('N.vectensis_Acat',((((('O.minuta_Acat','A.vastus_Acat'),((((((('D.melanogaster_vinc','M.musculus_vinc'),('B.floridae_vinc-b','B.floridae_vinc-a')),'N_vectensis_vinc'),(((('O.lobularis_vinc','O.carmela_vinc'),(('S.ciliatum_vinc-b','L.complicata_vinc-b'),('L.complicata_vinc-a','S.ciliatum_vinc-a'))),('A.queenslandica_vinc','P.ficiformis_vinc')),'M.leidyi_vinc')),'T.adhaerens_vinc'),('A.vastus_vinc','O.minuta_vinc')),('L.complicata_Acat','S.ciliatum_Acat'))),('O.lobularis_Acat','O.carmela_Acat')),('P.ficiformis_Acat','A_queenslandica_Acat')),('M.leidyi_Acat','T.adhaerens_Acat'))))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111214] END; BEGIN TREES; TITLE heuristic_tree_alignment_fig_S1C; LINK TAXA = TaxaForAnalysisStep22821; TREE 'Tree 20 from search (criterion: minimize Tree value using character matrix)' = [&R] (('M.musculus_Acat',('D_melanogaster_Acat',('N.vectensis_Acat',((((('O.minuta_Acat','A.vastus_Acat'),((((((('D.melanogaster_vinc','M.musculus_vinc'),('B.floridae_vinc-b','B.floridae_vinc-a')),'N_vectensis_vinc'),(((('A.queenslandica_vinc','P.ficiformis_vinc'),('O.lobularis_vinc','O.carmela_vinc')),(('S.ciliatum_vinc-b','L.complicata_vinc-b'),('L.complicata_vinc-a','S.ciliatum_vinc-a'))),'M.leidyi_vinc')),'T.adhaerens_vinc'),('A.vastus_vinc','O.minuta_vinc')),('L.complicata_Acat','S.ciliatum_Acat'))),('O.lobularis_Acat','O.carmela_Acat')),('P.ficiformis_Acat','A_queenslandica_Acat')),('M.leidyi_Acat','T.adhaerens_Acat'))))),'B.floridae_Acat'); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111208] END; BEGIN TREES; TITLE heuristic_tree_alignment_fig_S1C; LINK TAXA = TaxaForAnalysisStep22821; TREE 'Tree 27 from search (criterion: minimize Tree value using character matrix)' = [&R] ((('B.floridae_Acat','D_melanogaster_Acat'),('N.vectensis_Acat',((((('O.minuta_Acat','A.vastus_Acat'),((((((('M.musculus_vinc',('B.floridae_vinc-b','B.floridae_vinc-a')),'D.melanogaster_vinc'),'N_vectensis_vinc'),(((('A.queenslandica_vinc','P.ficiformis_vinc'),('O.lobularis_vinc','O.carmela_vinc')),(('S.ciliatum_vinc-b','L.complicata_vinc-b'),('L.complicata_vinc-a','S.ciliatum_vinc-a'))),'M.leidyi_vinc')),'T.adhaerens_vinc'),('A.vastus_vinc','O.minuta_vinc')),('L.complicata_Acat','S.ciliatum_Acat'))),('O.lobularis_Acat','O.carmela_Acat')),('P.ficiformis_Acat','A_queenslandica_Acat')),('M.leidyi_Acat','T.adhaerens_Acat')))),'M.musculus_Acat'); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111215] END; BEGIN TREES; TITLE heuristic_tree_alignment_fig_S1C; LINK TAXA = TaxaForAnalysisStep22821; TREE 'Tree 17 from search (criterion: minimize Tree value using character matrix)' = [&R] ('N.vectensis_Acat',((('B.floridae_Acat','D_melanogaster_Acat'),'M.musculus_Acat'),((((('O.minuta_Acat','A.vastus_Acat'),((((((('D.melanogaster_vinc','M.musculus_vinc'),('B.floridae_vinc-b','B.floridae_vinc-a')),'N_vectensis_vinc'),(((('A.queenslandica_vinc','P.ficiformis_vinc'),('O.lobularis_vinc','O.carmela_vinc')),(('S.ciliatum_vinc-b','L.complicata_vinc-b'),('L.complicata_vinc-a','S.ciliatum_vinc-a'))),'M.leidyi_vinc')),'T.adhaerens_vinc'),('A.vastus_vinc','O.minuta_vinc')),('L.complicata_Acat','S.ciliatum_Acat'))),('O.lobularis_Acat','O.carmela_Acat')),('P.ficiformis_Acat','A_queenslandica_Acat')),('M.leidyi_Acat','T.adhaerens_Acat')))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111205] END; BEGIN TREES; TITLE heuristic_tree_alignment_fig_S1C; LINK TAXA = TaxaForAnalysisStep22821; TREE 'Tree 25 from search (criterion: minimize Tree value using character matrix)' = [&R] ('D_melanogaster_Acat',(('M.musculus_Acat','B.floridae_Acat'),('N.vectensis_Acat',((((('O.minuta_Acat','A.vastus_Acat'),((((((('M.musculus_vinc',('B.floridae_vinc-b','B.floridae_vinc-a')),'D.melanogaster_vinc'),'N_vectensis_vinc'),(((('A.queenslandica_vinc','P.ficiformis_vinc'),('O.lobularis_vinc','O.carmela_vinc')),(('S.ciliatum_vinc-b','L.complicata_vinc-b'),('L.complicata_vinc-a','S.ciliatum_vinc-a'))),'M.leidyi_vinc')),'T.adhaerens_vinc'),('A.vastus_vinc','O.minuta_vinc')),('L.complicata_Acat','S.ciliatum_Acat'))),('O.lobularis_Acat','O.carmela_Acat')),('P.ficiformis_Acat','A_queenslandica_Acat')),('M.leidyi_Acat','T.adhaerens_Acat'))))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111213] END; BEGIN TREES; TITLE heuristic_tree_alignment_fig_S1C; LINK TAXA = TaxaForAnalysisStep22821; TREE 'Tree 15 from search (criterion: minimize Tree value using character matrix)' = [&R] (('N.vectensis_Acat',(('M.musculus_Acat','B.floridae_Acat'),'D_melanogaster_Acat')),((((('O.minuta_Acat','A.vastus_Acat'),((((((('M.musculus_vinc',('B.floridae_vinc-b','B.floridae_vinc-a')),'D.melanogaster_vinc'),'N_vectensis_vinc'),(((('A.queenslandica_vinc','P.ficiformis_vinc'),('O.lobularis_vinc','O.carmela_vinc')),(('S.ciliatum_vinc-b','L.complicata_vinc-b'),('L.complicata_vinc-a','S.ciliatum_vinc-a'))),'M.leidyi_vinc')),'T.adhaerens_vinc'),('A.vastus_vinc','O.minuta_vinc')),('L.complicata_Acat','S.ciliatum_Acat'))),('O.lobularis_Acat','O.carmela_Acat')),('P.ficiformis_Acat','A_queenslandica_Acat')),('M.leidyi_Acat','T.adhaerens_Acat'))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111203] END; BEGIN TREES; TITLE heuristic_tree_alignment_fig_S1C; LINK TAXA = TaxaForAnalysisStep22821; TREE 'Tree 1 from search (criterion: minimize Tree value using character matrix)' = [&R] ((('M.musculus_Acat','B.floridae_Acat'),'D_melanogaster_Acat'),('N.vectensis_Acat',((((('O.minuta_Acat','A.vastus_Acat'),((((((('D.melanogaster_vinc','M.musculus_vinc'),('B.floridae_vinc-b','B.floridae_vinc-a')),'N_vectensis_vinc'),(((('A.queenslandica_vinc','P.ficiformis_vinc'),('O.lobularis_vinc','O.carmela_vinc')),(('S.ciliatum_vinc-b','L.complicata_vinc-b'),('L.complicata_vinc-a','S.ciliatum_vinc-a'))),'M.leidyi_vinc')),'T.adhaerens_vinc'),('A.vastus_vinc','O.minuta_vinc')),('L.complicata_Acat','S.ciliatum_Acat'))),('O.lobularis_Acat','O.carmela_Acat')),('P.ficiformis_Acat','A_queenslandica_Acat')),('M.leidyi_Acat','T.adhaerens_Acat')))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111189] END; BEGIN TREES; TITLE heuristic_tree_alignment_fig_S1C; LINK TAXA = TaxaForAnalysisStep22821; TREE 'Tree 9 from search (criterion: minimize Tree value using character matrix)' = [&R] ((('M.musculus_Acat',('N.vectensis_Acat',((((('O.minuta_Acat','A.vastus_Acat'),((((((('D.melanogaster_vinc','M.musculus_vinc'),('B.floridae_vinc-b','B.floridae_vinc-a')),'N_vectensis_vinc'),(((('A.queenslandica_vinc','P.ficiformis_vinc'),('O.lobularis_vinc','O.carmela_vinc')),(('S.ciliatum_vinc-b','L.complicata_vinc-b'),('L.complicata_vinc-a','S.ciliatum_vinc-a'))),'M.leidyi_vinc')),'T.adhaerens_vinc'),('A.vastus_vinc','O.minuta_vinc')),('L.complicata_Acat','S.ciliatum_Acat'))),('O.lobularis_Acat','O.carmela_Acat')),('P.ficiformis_Acat','A_queenslandica_Acat')),('M.leidyi_Acat','T.adhaerens_Acat')))),'B.floridae_Acat'),'D_melanogaster_Acat'); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111197] END; BEGIN TREES; TITLE heuristic_tree_alignment_fig_S1C; LINK TAXA = TaxaForAnalysisStep22821; TREE 'Tree 19 from search (criterion: minimize Tree value using character matrix)' = [&R] ('N.vectensis_Acat',((('M.musculus_Acat','B.floridae_Acat'),'D_melanogaster_Acat'),((((('O.minuta_Acat','A.vastus_Acat'),((((((('D.melanogaster_vinc','M.musculus_vinc'),('B.floridae_vinc-b','B.floridae_vinc-a')),'N_vectensis_vinc'),(((('O.lobularis_vinc','O.carmela_vinc'),(('S.ciliatum_vinc-b','L.complicata_vinc-b'),('L.complicata_vinc-a','S.ciliatum_vinc-a'))),('A.queenslandica_vinc','P.ficiformis_vinc')),'M.leidyi_vinc')),'T.adhaerens_vinc'),('A.vastus_vinc','O.minuta_vinc')),('L.complicata_Acat','S.ciliatum_Acat'))),('O.lobularis_Acat','O.carmela_Acat')),('P.ficiformis_Acat','A_queenslandica_Acat')),('M.leidyi_Acat','T.adhaerens_Acat')))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111207] END; BEGIN TREES; TITLE heuristic_tree_alignment_fig_S1C; LINK TAXA = TaxaForAnalysisStep22821; TREE 'Tree 2 from search (criterion: minimize Tree value using character matrix)' = [&R] (('N.vectensis_Acat',(('M.musculus_Acat','B.floridae_Acat'),'D_melanogaster_Acat')),((((('O.minuta_Acat','A.vastus_Acat'),((((((('D.melanogaster_vinc','M.musculus_vinc'),('B.floridae_vinc-b','B.floridae_vinc-a')),'N_vectensis_vinc'),(((('A.queenslandica_vinc','P.ficiformis_vinc'),('O.lobularis_vinc','O.carmela_vinc')),(('S.ciliatum_vinc-b','L.complicata_vinc-b'),('L.complicata_vinc-a','S.ciliatum_vinc-a'))),'M.leidyi_vinc')),'T.adhaerens_vinc'),('A.vastus_vinc','O.minuta_vinc')),('L.complicata_Acat','S.ciliatum_Acat'))),('O.lobularis_Acat','O.carmela_Acat')),('P.ficiformis_Acat','A_queenslandica_Acat')),('M.leidyi_Acat','T.adhaerens_Acat'))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111190] END; BEGIN TREES; TITLE heuristic_tree_alignment_fig_S1C; LINK TAXA = TaxaForAnalysisStep22821; TREE 'Tree 100 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('O.minuta_Acat','A.vastus_Acat'),((((((('M.musculus_vinc',('B.floridae_vinc-b','B.floridae_vinc-a')),'D.melanogaster_vinc'),'N_vectensis_vinc'),(((('O.lobularis_vinc','O.carmela_vinc'),(('S.ciliatum_vinc-b','L.complicata_vinc-b'),('L.complicata_vinc-a','S.ciliatum_vinc-a'))),('A.queenslandica_vinc','P.ficiformis_vinc')),'M.leidyi_vinc')),'T.adhaerens_vinc'),('A.vastus_vinc','O.minuta_vinc')),('L.complicata_Acat','S.ciliatum_Acat'))),('O.lobularis_Acat','O.carmela_Acat')),('P.ficiformis_Acat','A_queenslandica_Acat')),(('N.vectensis_Acat',(('M.musculus_Acat','B.floridae_Acat'),'D_melanogaster_Acat')),('M.leidyi_Acat','T.adhaerens_Acat'))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111218] END; BEGIN TREES; TITLE heuristic_tree_alignment_fig_S1C; LINK TAXA = TaxaForAnalysisStep22821; TREE 'Tree 14 from search (criterion: minimize Tree value using character matrix)' = [&R] (('N.vectensis_Acat',('M.musculus_Acat',('B.floridae_Acat','D_melanogaster_Acat'))),((((('O.minuta_Acat','A.vastus_Acat'),((((((('D.melanogaster_vinc','M.musculus_vinc'),('B.floridae_vinc-b','B.floridae_vinc-a')),'N_vectensis_vinc'),(((('A.queenslandica_vinc','P.ficiformis_vinc'),('O.lobularis_vinc','O.carmela_vinc')),(('S.ciliatum_vinc-b','L.complicata_vinc-b'),('L.complicata_vinc-a','S.ciliatum_vinc-a'))),'M.leidyi_vinc')),'T.adhaerens_vinc'),('A.vastus_vinc','O.minuta_vinc')),('L.complicata_Acat','S.ciliatum_Acat'))),('O.lobularis_Acat','O.carmela_Acat')),('P.ficiformis_Acat','A_queenslandica_Acat')),('M.leidyi_Acat','T.adhaerens_Acat'))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111202] END; BEGIN TREES; TITLE heuristic_tree_alignment_fig_S1C; LINK TAXA = TaxaForAnalysisStep22821; TREE 'Tree 3 from search (criterion: minimize Tree value using character matrix)' = [&R] ('N.vectensis_Acat',((('M.musculus_Acat','B.floridae_Acat'),'D_melanogaster_Acat'),((((('O.minuta_Acat','A.vastus_Acat'),((((((('D.melanogaster_vinc','M.musculus_vinc'),('B.floridae_vinc-b','B.floridae_vinc-a')),'N_vectensis_vinc'),(((('A.queenslandica_vinc','P.ficiformis_vinc'),('O.lobularis_vinc','O.carmela_vinc')),(('S.ciliatum_vinc-b','L.complicata_vinc-b'),('L.complicata_vinc-a','S.ciliatum_vinc-a'))),'M.leidyi_vinc')),'T.adhaerens_vinc'),('A.vastus_vinc','O.minuta_vinc')),('L.complicata_Acat','S.ciliatum_Acat'))),('O.lobularis_Acat','O.carmela_Acat')),('P.ficiformis_Acat','A_queenslandica_Acat')),('M.leidyi_Acat','T.adhaerens_Acat')))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111191] END; BEGIN TREES; TITLE heuristic_tree_alignment_fig_S1C; LINK TAXA = TaxaForAnalysisStep22821; TREE 'Tree 8 from search (criterion: minimize Tree value using character matrix)' = [&R] (('B.floridae_Acat','D_melanogaster_Acat'),('M.musculus_Acat',('N.vectensis_Acat',((((('O.minuta_Acat','A.vastus_Acat'),((((((('D.melanogaster_vinc','M.musculus_vinc'),('B.floridae_vinc-b','B.floridae_vinc-a')),'N_vectensis_vinc'),(((('A.queenslandica_vinc','P.ficiformis_vinc'),('O.lobularis_vinc','O.carmela_vinc')),(('S.ciliatum_vinc-b','L.complicata_vinc-b'),('L.complicata_vinc-a','S.ciliatum_vinc-a'))),'M.leidyi_vinc')),'T.adhaerens_vinc'),('A.vastus_vinc','O.minuta_vinc')),('L.complicata_Acat','S.ciliatum_Acat'))),('O.lobularis_Acat','O.carmela_Acat')),('P.ficiformis_Acat','A_queenslandica_Acat')),('M.leidyi_Acat','T.adhaerens_Acat'))))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111196] END; BEGIN TREES; TITLE heuristic_tree_alignment_fig_S1C; LINK TAXA = TaxaForAnalysisStep22821; TREE 'Tree 28 from search (criterion: minimize Tree value using character matrix)' = [&R] ((('B.floridae_Acat','D_melanogaster_Acat'),('N.vectensis_Acat',((((('O.minuta_Acat','A.vastus_Acat'),((((((('D.melanogaster_vinc','M.musculus_vinc'),('B.floridae_vinc-b','B.floridae_vinc-a')),'N_vectensis_vinc'),(((('O.lobularis_vinc','O.carmela_vinc'),(('S.ciliatum_vinc-b','L.complicata_vinc-b'),('L.complicata_vinc-a','S.ciliatum_vinc-a'))),('A.queenslandica_vinc','P.ficiformis_vinc')),'M.leidyi_vinc')),'T.adhaerens_vinc'),('A.vastus_vinc','O.minuta_vinc')),('L.complicata_Acat','S.ciliatum_Acat'))),('O.lobularis_Acat','O.carmela_Acat')),('P.ficiformis_Acat','A_queenslandica_Acat')),('M.leidyi_Acat','T.adhaerens_Acat')))),'M.musculus_Acat'); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111216] END; BEGIN TREES; TITLE heuristic_tree_alignment_fig_S1C; LINK TAXA = TaxaForAnalysisStep22821; TREE 'Tree 29 from search (criterion: minimize Tree value using character matrix)' = [&R] ((('B.floridae_Acat','D_melanogaster_Acat'),'M.musculus_Acat'),('N.vectensis_Acat',((((('O.minuta_Acat','A.vastus_Acat'),((((((('M.musculus_vinc',('B.floridae_vinc-b','B.floridae_vinc-a')),'D.melanogaster_vinc'),'N_vectensis_vinc'),(((('A.queenslandica_vinc','P.ficiformis_vinc'),('O.lobularis_vinc','O.carmela_vinc')),(('S.ciliatum_vinc-b','L.complicata_vinc-b'),('L.complicata_vinc-a','S.ciliatum_vinc-a'))),'M.leidyi_vinc')),'T.adhaerens_vinc'),('A.vastus_vinc','O.minuta_vinc')),('L.complicata_Acat','S.ciliatum_Acat'))),('O.lobularis_Acat','O.carmela_Acat')),('P.ficiformis_Acat','A_queenslandica_Acat')),('M.leidyi_Acat','T.adhaerens_Acat')))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111217] END; BEGIN TREES; TITLE heuristic_tree_alignment_fig_S1C; LINK TAXA = TaxaForAnalysisStep22821; TREE 'Tree 12 from search (criterion: minimize Tree value using character matrix)' = [&R] (((((('O.minuta_Acat','A.vastus_Acat'),((((((('D.melanogaster_vinc','M.musculus_vinc'),('B.floridae_vinc-b','B.floridae_vinc-a')),'N_vectensis_vinc'),(((('A.queenslandica_vinc','P.ficiformis_vinc'),('O.lobularis_vinc','O.carmela_vinc')),(('S.ciliatum_vinc-b','L.complicata_vinc-b'),('L.complicata_vinc-a','S.ciliatum_vinc-a'))),'M.leidyi_vinc')),'T.adhaerens_vinc'),('A.vastus_vinc','O.minuta_vinc')),('L.complicata_Acat','S.ciliatum_Acat'))),('O.lobularis_Acat','O.carmela_Acat')),('P.ficiformis_Acat','A_queenslandica_Acat')),('N.vectensis_Acat',(('M.musculus_Acat','B.floridae_Acat'),'D_melanogaster_Acat'))),('M.leidyi_Acat','T.adhaerens_Acat')); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111200] END; BEGIN TREES; TITLE heuristic_tree_alignment_fig_S1C; LINK TAXA = TaxaForAnalysisStep22821; TREE 'Tree 6 from search (criterion: minimize Tree value using character matrix)' = [&R] ((('B.floridae_Acat','D_melanogaster_Acat'),('N.vectensis_Acat',((((('O.minuta_Acat','A.vastus_Acat'),((((((('D.melanogaster_vinc','M.musculus_vinc'),('B.floridae_vinc-b','B.floridae_vinc-a')),'N_vectensis_vinc'),(((('A.queenslandica_vinc','P.ficiformis_vinc'),('O.lobularis_vinc','O.carmela_vinc')),(('S.ciliatum_vinc-b','L.complicata_vinc-b'),('L.complicata_vinc-a','S.ciliatum_vinc-a'))),'M.leidyi_vinc')),'T.adhaerens_vinc'),('A.vastus_vinc','O.minuta_vinc')),('L.complicata_Acat','S.ciliatum_Acat'))),('O.lobularis_Acat','O.carmela_Acat')),('P.ficiformis_Acat','A_queenslandica_Acat')),('M.leidyi_Acat','T.adhaerens_Acat')))),'M.musculus_Acat'); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111194] END; BEGIN TREES; TITLE heuristic_tree_alignment_fig_S1C; LINK TAXA = TaxaForAnalysisStep22821; TREE 'Tree 5 from search (criterion: minimize Tree value using character matrix)' = [&R] ('D_melanogaster_Acat',(('M.musculus_Acat','B.floridae_Acat'),('N.vectensis_Acat',((((('O.minuta_Acat','A.vastus_Acat'),((((((('D.melanogaster_vinc','M.musculus_vinc'),('B.floridae_vinc-b','B.floridae_vinc-a')),'N_vectensis_vinc'),(((('A.queenslandica_vinc','P.ficiformis_vinc'),('O.lobularis_vinc','O.carmela_vinc')),(('S.ciliatum_vinc-b','L.complicata_vinc-b'),('L.complicata_vinc-a','S.ciliatum_vinc-a'))),'M.leidyi_vinc')),'T.adhaerens_vinc'),('A.vastus_vinc','O.minuta_vinc')),('L.complicata_Acat','S.ciliatum_Acat'))),('O.lobularis_Acat','O.carmela_Acat')),('P.ficiformis_Acat','A_queenslandica_Acat')),('M.leidyi_Acat','T.adhaerens_Acat'))))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111193] END; BEGIN TREES; TITLE heuristic_tree_alignment_fig_S1C; LINK TAXA = TaxaForAnalysisStep22821; TREE 'Tree 10 from search (criterion: minimize Tree value using character matrix)' = [&R] ((('M.musculus_Acat','B.floridae_Acat'),'D_melanogaster_Acat'),('N.vectensis_Acat',((((('O.minuta_Acat','A.vastus_Acat'),((((((('M.musculus_vinc',('B.floridae_vinc-b','B.floridae_vinc-a')),'D.melanogaster_vinc'),'N_vectensis_vinc'),(((('A.queenslandica_vinc','P.ficiformis_vinc'),('O.lobularis_vinc','O.carmela_vinc')),(('S.ciliatum_vinc-b','L.complicata_vinc-b'),('L.complicata_vinc-a','S.ciliatum_vinc-a'))),'M.leidyi_vinc')),'T.adhaerens_vinc'),('A.vastus_vinc','O.minuta_vinc')),('L.complicata_Acat','S.ciliatum_Acat'))),('O.lobularis_Acat','O.carmela_Acat')),('P.ficiformis_Acat','A_queenslandica_Acat')),('M.leidyi_Acat','T.adhaerens_Acat')))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111198] END; BEGIN TREES; TITLE heuristic_tree_alignment_fig_S1C; LINK TAXA = TaxaForAnalysisStep22821; TREE 'Tree 4 from search (criterion: minimize Tree value using character matrix)' = [&R] (('D_melanogaster_Acat',('N.vectensis_Acat',((((('O.minuta_Acat','A.vastus_Acat'),((((((('D.melanogaster_vinc','M.musculus_vinc'),('B.floridae_vinc-b','B.floridae_vinc-a')),'N_vectensis_vinc'),(((('A.queenslandica_vinc','P.ficiformis_vinc'),('O.lobularis_vinc','O.carmela_vinc')),(('S.ciliatum_vinc-b','L.complicata_vinc-b'),('L.complicata_vinc-a','S.ciliatum_vinc-a'))),'M.leidyi_vinc')),'T.adhaerens_vinc'),('A.vastus_vinc','O.minuta_vinc')),('L.complicata_Acat','S.ciliatum_Acat'))),('O.lobularis_Acat','O.carmela_Acat')),('P.ficiformis_Acat','A_queenslandica_Acat')),('M.leidyi_Acat','T.adhaerens_Acat')))),('M.musculus_Acat','B.floridae_Acat')); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111192] END; BEGIN TREES; TITLE heuristic_tree_alignment_fig_S1C; LINK TAXA = TaxaForAnalysisStep22821; TREE 'Tree 7 from search (criterion: minimize Tree value using character matrix)' = [&R] ((('B.floridae_Acat','D_melanogaster_Acat'),'M.musculus_Acat'),('N.vectensis_Acat',((((('O.minuta_Acat','A.vastus_Acat'),((((((('D.melanogaster_vinc','M.musculus_vinc'),('B.floridae_vinc-b','B.floridae_vinc-a')),'N_vectensis_vinc'),(((('A.queenslandica_vinc','P.ficiformis_vinc'),('O.lobularis_vinc','O.carmela_vinc')),(('S.ciliatum_vinc-b','L.complicata_vinc-b'),('L.complicata_vinc-a','S.ciliatum_vinc-a'))),'M.leidyi_vinc')),'T.adhaerens_vinc'),('A.vastus_vinc','O.minuta_vinc')),('L.complicata_Acat','S.ciliatum_Acat'))),('O.lobularis_Acat','O.carmela_Acat')),('P.ficiformis_Acat','A_queenslandica_Acat')),('M.leidyi_Acat','T.adhaerens_Acat')))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111195] END; BEGIN TREES; TITLE heuristic_tree_alignment_fig_S1C; LINK TAXA = TaxaForAnalysisStep22821; TREE 'Tree 24 from search (criterion: minimize Tree value using character matrix)' = [&R] (('D_melanogaster_Acat',('M.musculus_Acat',('N.vectensis_Acat',((((('O.minuta_Acat','A.vastus_Acat'),((((((('D.melanogaster_vinc','M.musculus_vinc'),('B.floridae_vinc-b','B.floridae_vinc-a')),'N_vectensis_vinc'),(((('A.queenslandica_vinc','P.ficiformis_vinc'),('O.lobularis_vinc','O.carmela_vinc')),(('S.ciliatum_vinc-b','L.complicata_vinc-b'),('L.complicata_vinc-a','S.ciliatum_vinc-a'))),'M.leidyi_vinc')),'T.adhaerens_vinc'),('A.vastus_vinc','O.minuta_vinc')),('L.complicata_Acat','S.ciliatum_Acat'))),('O.lobularis_Acat','O.carmela_Acat')),('P.ficiformis_Acat','A_queenslandica_Acat')),('M.leidyi_Acat','T.adhaerens_Acat'))))),'B.floridae_Acat'); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111212] END; BEGIN TREES; TITLE heuristic_tree_alignment_fig_S1C; LINK TAXA = TaxaForAnalysisStep22821; TREE 'Tree 23 from search (criterion: minimize Tree value using character matrix)' = [&R] (('D_melanogaster_Acat',('N.vectensis_Acat',((((('O.minuta_Acat','A.vastus_Acat'),((((((('D.melanogaster_vinc','M.musculus_vinc'),('B.floridae_vinc-b','B.floridae_vinc-a')),'N_vectensis_vinc'),(((('O.lobularis_vinc','O.carmela_vinc'),(('S.ciliatum_vinc-b','L.complicata_vinc-b'),('L.complicata_vinc-a','S.ciliatum_vinc-a'))),('A.queenslandica_vinc','P.ficiformis_vinc')),'M.leidyi_vinc')),'T.adhaerens_vinc'),('A.vastus_vinc','O.minuta_vinc')),('L.complicata_Acat','S.ciliatum_Acat'))),('O.lobularis_Acat','O.carmela_Acat')),('P.ficiformis_Acat','A_queenslandica_Acat')),('M.leidyi_Acat','T.adhaerens_Acat')))),('M.musculus_Acat','B.floridae_Acat')); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111211] END; BEGIN TREES; TITLE heuristic_tree_alignment_fig_S1C; LINK TAXA = TaxaForAnalysisStep22821; TREE 'Tree 21 from search (criterion: minimize Tree value using character matrix)' = [&R] ('M.musculus_Acat',(('D_melanogaster_Acat',('N.vectensis_Acat',((((('O.minuta_Acat','A.vastus_Acat'),((((((('D.melanogaster_vinc','M.musculus_vinc'),('B.floridae_vinc-b','B.floridae_vinc-a')),'N_vectensis_vinc'),(((('A.queenslandica_vinc','P.ficiformis_vinc'),('O.lobularis_vinc','O.carmela_vinc')),(('S.ciliatum_vinc-b','L.complicata_vinc-b'),('L.complicata_vinc-a','S.ciliatum_vinc-a'))),'M.leidyi_vinc')),'T.adhaerens_vinc'),('A.vastus_vinc','O.minuta_vinc')),('L.complicata_Acat','S.ciliatum_Acat'))),('O.lobularis_Acat','O.carmela_Acat')),('P.ficiformis_Acat','A_queenslandica_Acat')),('M.leidyi_Acat','T.adhaerens_Acat')))),'B.floridae_Acat')); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111209] END; BEGIN TREES; TITLE heuristic_tree_alignment_fig_S1C; LINK TAXA = TaxaForAnalysisStep22821; TREE 'Tree 18 from search (criterion: minimize Tree value using character matrix)' = [&R] ('N.vectensis_Acat',((('M.musculus_Acat','B.floridae_Acat'),'D_melanogaster_Acat'),((((('O.minuta_Acat','A.vastus_Acat'),((((((('M.musculus_vinc',('B.floridae_vinc-b','B.floridae_vinc-a')),'D.melanogaster_vinc'),'N_vectensis_vinc'),(((('A.queenslandica_vinc','P.ficiformis_vinc'),('O.lobularis_vinc','O.carmela_vinc')),(('S.ciliatum_vinc-b','L.complicata_vinc-b'),('L.complicata_vinc-a','S.ciliatum_vinc-a'))),'M.leidyi_vinc')),'T.adhaerens_vinc'),('A.vastus_vinc','O.minuta_vinc')),('L.complicata_Acat','S.ciliatum_Acat'))),('O.lobularis_Acat','O.carmela_Acat')),('P.ficiformis_Acat','A_queenslandica_Acat')),('M.leidyi_Acat','T.adhaerens_Acat')))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111206] END;