#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; 2:16 GMT TreeBASE (cc) 1994-2008 Study reference: Watanabe H., Schmidt H.A., Kuhn A., Höger S.K., Kocagöz Y., Laumann-lipp N., Özbek S., & Holstein T.W. 2014. Nodal signalling determines biradial asymmetry in Hydra. Nature, . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S16190] [ The following blocks are input data for analysis step 14285 ] BEGIN TAXA; TITLE TaxaForAnalysisStep14285; DIMENSIONS NTAX=164; TAXLABELS Acropora_digitifera_Alx Acropora_digitifera_Arx Acropora_digitifera_DmbxB Acropora_digitifera_DmbxD Acropora_digitifera_Gsc 'Acropora digitifera Mixer-like' Acropora_digitifera_Otp Acropora_digitifera_OtxA Acropora_digitifera_OtxB Acropora_digitifera_OtxC Acropora_digitifera_OtxD 'Acropora digitifera Pax3/7a' 'Acropora digitifera Pax3/7b' Acropora_digitifera_Pax6a Acropora_digitifera_Pax6b Acropora_digitifera_Pitx Acropora_digitifera_Rx Acropora_digitifera_Unc4.1 Acropora_digitifera_Unc4c Acropora_millepora_1217446 Acropora_millepora_Alx Acropora_millepora_Arx Acropora_millepora_DmbxB Acropora_millepora_Gsc 'Acropora millepora Mixer-like' Acropora_millepora_Otp Acropora_millepora_OtxA Acropora_millepora_OtxB 'Acropora millepora Pax3/7a' 'Acropora millepora Pax3/7b' Acropora_millepora_Pax6a Acropora_millepora_Pitx Acropora_millepora_Rx Acropora_millepora_Unc4.1 Acropora_millepora_Unc4c 'Amphimedon queenslandica Arx-likeA' 'Amphimedon queenslandica Arx-likeB' 'Amphimedon queenslandica Arx-likeC' 'Branchiostoma floridae Alx-like' Branchiostoma_floridae_Dmbx Branchiostoma_floridae_Gsc Branchiostoma_floridae_Otx 'Branchiostoma floridae Pax3/7' Branchiostoma_floridae_Pax6 Branchiostoma_floridae_Pitx2 Branchiostoma_floridae_Q50 Branchiostoma_floridae_Rax Branchiostoma_floridae_Rx Branchiostoma_floridae_Unc4 Branchiostoma_floridae_Unc4c Ciona_intestinalis_118343665 Ciona_intestinalis_Gsc Ciona_intestinalis_OTX Ciona_intestinalis_Otp Ciona_intestinalis_Pitx Cladonema_pacificum_ArxA Cladonema_pacificum_ArxB Cladonema_pacificum_ArxC Cladonema_pacificum_ArxD Cladonema_pacificum_Gsc Cladonema_pacificum_Otp Cladonema_pacificum_OtxA Cladonema_pacificum_OtxB Cladonema_pacificum_Pitx Danio_rerio_Alx1 'Danio rerio Arx-like' Danio_rerio_Dmbx1 Danio_rerio_Gsc Danio_rerio_Mixer Danio_rerio_OTX1b Danio_rerio_OtpB Danio_rerio_Otx2 Danio_rerio_Pax3 Danio_rerio_Pax6 Danio_rerio_Pitx2 Danio_rerio_Pitx3 Danio_rerio_Rx1 Danio_rerio_Uncx4.1 Drosophila_melanogaster_Alx Drosophila_melanogaster_Eyegone Drosophila_melanogaster_Gooseberry Drosophila_melanogaster_Gsc Drosophila_melanogaster_Otp Drosophila_melanogaster_Otx Drosophila_melanogaster_Ptx1 Drosophila_melanogaster_Rx Drosophila_melanogaster_Unc4 'Hydra magnipapillata Arx-like' Hydra_magnipapillata_Dmbx Hydra_magnipapillata_Gsc Hydra_magnipapillata_Otp 'Hydra magnipapillata Otx1/2' Hydra_magnipapillata_OtxA Hydra_magnipapillata_OtxB Hydra_magnipapillata_Pitx Hydra_magnipapillata_Rx Hydra_magnipapillata_Unc4.1 Lottia_gigantea_Dmbx1 Lottia_gigantea_Gsc Lottia_gigantea_Otp Lottia_gigantea_Otx 'Lottia gigantea Pax3/7' Lottia_gigantea_Pax6 Lottia_gigantea_Pitx2 Lottia_gigantea_Rx Lottia_gigantea_Unc4.1 Mnemiopsis_leidyi_PRD43 Mnemiopsis_leidyi_PRD61 Mus_musculus_ALX1 Mus_musculus_Dmbx1a Mus_musculus_Gsc Mus_musculus_MixerL1 Mus_musculus_OTP Mus_musculus_OTX1 Mus_musculus_Pax6 Mus_musculus_Pax7 Mus_musculus_Pitx2 Mus_musculus_Rx Mus_musculus_Uncx4.1 Nematostella_vectensis_Alx Nematostella_vectensis_Arx Nematostella_vectensis_DmbxA Nematostella_vectensis_DmbxB Nematostella_vectensis_DmbxC Nematostella_vectensis_DmbxD Nematostella_vectensis_Gsc 'Nematostella vectensis Mixer-like' Nematostella_vectensis_Otp Nematostella_vectensis_OtxA Nematostella_vectensis_OtxB Nematostella_vectensis_OtxC Nematostella_vectensis_PaxB Nematostella_vectensis_PaxC Nematostella_vectensis_PaxD Nematostella_vectensis_PaxD2 Nematostella_vectensis_Pitx Nematostella_vectensis_Rx Nematostella_vectensis_Unc4.1 Nematostella_vectensis_Unc4c 'Oscarella carmela Arx-likeA' 'Oscarella carmela Arx-likeB' 'Oscarella carmela Arx-likeC' Saccoglossus_kowalevskii_Alx Saccoglossus_kowalevskii_Dmbx Saccoglossus_kowalevskii_Eyegone Saccoglossus_kowalevskii_Otp Saccoglossus_kowalevskii_Otx Saccoglossus_kowalevskii_Pax6 Saccoglossus_kowalevskii_Pitx2 Saccoglossus_kowalevskii_Rx 'Saccoglossus kowalevskii Rx-like' Saccoglossus_kowalevskii_Unc4.1 'Saccoglossus kowalevskii Unc4c-like' Tribolium_castaneum_Alx Tribolium_castaneum_Gsc Tribolium_castaneum_Otx1 Tribolium_castaneum_Otx2 Tribolium_castaneum_Pitx1 Tribolium_castaneum_Rx Trichoplax_adhaerens_196002946 Trichoplax_adhaerens_Gsc Trichoplax_adhaerens_Otp Trichoplax_adhaerens_Pitx Trichoplax_adhaerens_Rx ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M23501] TITLE 'Prd/Pitx transcription factor gene superfamily alignment'; LINK TAXA = TaxaForAnalysisStep14285; DIMENSIONS NCHAR=64; 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 ] [ . . . . . . ] Acropora_digitifera_Alx KRKKRRNRTTFTSFQLEEMERIFQKTHYPDVYTREQLALRCDLTEARVQV-WFQNRRAKWRKRE Acropora_digitifera_Arx KRKQRRYRTTFTSLQLEELERAFSKTHYPDVFTREALALKIDLTEARVQV-WFQNRRAKWRKRE Acropora_digitifera_DmbxB RRAPRRSRTAFTHQQLGILEKAFSKTHYPDVELREQLASKTNLQESRIQV-WFKNRRAKYRKEV Acropora_digitifera_DmbxD GRKIRRTRTTFNQFQLETLERTFARTHYPDLMLREQLAAYTNLPESRVQV-WFKNRRAKYRKLK Acropora_digitifera_Gsc PKRKRRHRTIFTEEQLDLLEGTFQKTHYPDVLLREELAIKVALKEERVEV-WFKNRRAKWRKQK 'Acropora digitifera Mixer-like' KQDVKRKRKNLTKEQLEILESVYRKEKYPHMDDRIKLEKSTNLSEDRIQV-WFQNRRAKDRKKI Acropora_digitifera_Otp GVKQKRHRTRFTPAQLNELERCFARTHYPDVFMREDLAARIGLTESRVQVKALKNVDVR----- Acropora_digitifera_OtxA PRKQRRERTTFTKAQLEILEELFTKTKYPDIFMREEVAMKINLPESRVQV-WFKNRRAKCRQLD Acropora_digitifera_OtxB PRKQRRERTTFTKAQLEILDELFAKTKYPDIFMREEVAMKINLPESRVQV-WFKNRRAKFRQQT Acropora_digitifera_OtxC PRKQRRERTTFTKAQLEILEELFSKTKYPDIFMREEVAMKINLPESRVQV-WFKNRRAKVRQQS Acropora_digitifera_OtxD PRKQRRERTTFTKAQLKLLDELFAKTKYPDIFMREELALKINLPESRVQV-WFKNKRAKCRQQT 'Acropora digitifera Pax3/7a' ARKQRRSRTKFTHAQLNALEKAFQKTQYPDVYTREELAHRLSLTEARVQV-WFSNRRARLRKKD 'Acropora digitifera Pax3/7b' SRKPRRGRTKFSLKQVDELEKAFAKTHYPDVYTREELAQRLDLSEARVQV-WFSNRRARLRKEE Acropora_digitifera_Pax6a HKIVRRQRTTFSGEQIEQLEKTFEKTHYPDVFTREKLAQDVDLSEARIQV-WFSNRRAKWRKQE Acropora_digitifera_Pax6b ---LRRNRTTFTSEQLDILEREFEKTHYPGINTREELATKTKLSEARVQV-WFSNRRAKWRRTQ Acropora_digitifera_Pitx KRKQRRQRTHFTSYQLQEMEAMFARNRYPDMAVREDIALWTSLTEARVRV-WFKNRRAKWRKKE Acropora_digitifera_Rx TKKHRRNRTTFTTFQLHELEQAFEKSHYPDVYTREELALKIDLPEVRVQV-WFQNRRAKWRRQE Acropora_digitifera_Unc4.1 LPKKRRSRTNFDAWQLGELERVFKKTQYPDVFTREALALKLDLLESRVQV-WFQNRRAKLRREE Acropora_digitifera_Unc4c KPRRMRVRTNFSPWQLEQLERAFETTHYPDVFMREALALRLDLTEARVQV-WFQNRRAKWRKRE Acropora_millepora_1217446 RSYQRRNRTKFTPEQIEELESAFKKTQYPDALTREELAERLHISESKIQV-------------- Acropora_millepora_Alx KRKKRRNRTTFTSFQLEEMERIFQKTHYPDVYTREQLALRCDLTEARVQV-WFQNRRAKWRKRE Acropora_millepora_Arx KRKQRRYRTTFTSLQLEELERAFSKTHYPDVFTREALALKIDLTEARVQV-WFQNRRAKWRKRE Acropora_millepora_DmbxB RRAPRRSRTAFTHQQLGILEKAFSKTHYPDVELREQLASKTNLQESRIQV-WFKNRRAKYRKEV Acropora_millepora_Gsc PKRKRRHRTIFTEEQLDLLEGTFQKTHYPDVLLREELAIKVALKEERVEV-WFKNRRAKWRKQK 'Acropora millepora Mixer-like' KQDVKRKRKNLTKEQLEILESVYKKEKYPHMDDRIKLEKSTNLSEDRIQV-WFQNRRAKDRKRI Acropora_millepora_Otp GVKQKRHRTRFTPAQLNELERCFARTHYPDVFMREDLAARIGLTESRVQVKALKNVDVRLT--- Acropora_millepora_OtxA PRKQRRERTTFTKAQLEILEELFTKTKYPDIFMREEVAMKINLPESRVQV-WFKNRRAKCRQLD Acropora_millepora_OtxB PRKQRRERTTFTKAQLEILDELFAKTKYPDIFMREEVAMKINLPESRVQV-WFKNRRAKFRQQT 'Acropora millepora Pax3/7a' ARKQRRSRTKFTHAQLNALEKAFQKTQYPDVYTREELAHRLSLTEARVQV-WFSNRRARLRKKD 'Acropora millepora Pax3/7b' SRKPRRGRTKFSLKQVDELEKAFAKTHYPDVYTREELAQRLDLSEARVQV-WFSNRRARLRKEE Acropora_millepora_Pax6a HKIVRRQRTTFSGEQIEQLEKTFEKTHYPDVFTREKLAQDVDLSEARIQV-WFSNRRAKWRKQE Acropora_millepora_Pitx KRKQRRQRTHFTSYQLQEMEAMFARNRYPDMAVREDIALWTSLTEARVRV-WFKNRRAKWRKKE Acropora_millepora_Rx TKKHRRNRTTFTTFQLHELEQAFEKSHYPDVYTREELALKIDLPEVRVQV-WFQNRRAKWRRQE Acropora_millepora_Unc4.1 LPKKRRSRTNFDAWQLGELERVFKKTQYPDVFTREALALKLDLLESRVQV-WFQNRRAKLRREE Acropora_millepora_Unc4c KPRRMRVRTNFSPWQLEQLERAFETTHYPDVFMREALALRLDLTEARVQV-WFQNRRAKWRKRE 'Amphimedon queenslandica Arx-likeA' KRQQRRFRTTFTSYQLQELEAAFAKTHYPDVFMREDLALRINLTEARVQV-WFQNRRAKWRRAQ 'Amphimedon queenslandica Arx-likeB' KGKQRRHRTNFTSHQLEELEKAFEKTRYPDVFMREELAMKISLTEARVQV-WFQNRRAKWRKAE 'Amphimedon queenslandica Arx-likeC' IMKSKRNRTTFTAHQLDELEMIFRQTHYPDVLLREKLAQRIGLPESRVQV-WFQNRRAKWRKRE 'Branchiostoma floridae Alx-like' KKKKRRNRTTFTSFQLEEMERVFQKTHYPDVYMREQLALRADLTEARVQV-WFQNRRAKWRKKE Branchiostoma_floridae_Dmbx HRKQRRSRTAFTSQQLAALEKCFQKTHYPDVVMRERLAMCTNLPESRVQV-WFKNRRAKWRKRQ Branchiostoma_floridae_Gsc -RRKRRHRTIFTEEQLELLEKTFEKTHYPDVLLREELAMKVELKEERVEV-WFKNRRAKWRKQQ Branchiostoma_floridae_Otx PRKQRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQV-WFKNRRAKCRQQA 'Branchiostoma floridae Pax3/7' KRKQRRSRTTFTPEQLEELEKAFERTHYPDIYTREELAQRTKLTEARVQV-WFSNRRARWRKQQ Branchiostoma_floridae_Pax6 KRKLQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQV-WFSNRRAKWRREE Branchiostoma_floridae_Pitx2 RRRQRRQRTHFTSQQLQELEASFARNRYPDMATREEIAAWTNLTEARVRV-WFKNRRAKWRKRE Branchiostoma_floridae_Q50 KRKQRRYRTTFTSYQLEELERAFAKTHYPDVFTREELAMRVDLTEARVQV-WFQNRRAKWRKRE Branchiostoma_floridae_Rax KKKHRRNRTTFTTFQLHELERAFEKSHYPDVYSREELAMKINLPEVRVQV-WFQNRRAKWRRQE Branchiostoma_floridae_Rx GEKPKRNRTTFSTRQLQELERAFRQTHYPDIFMREELAMRVNLPESRVQV-WFQNRRAKWRKRE Branchiostoma_floridae_Unc4 PPKRRRTRTNFNSWQLEELERAFQESHYPDVFMREALALRLDLVESRVQV-WFQNRRAKWRKKE Branchiostoma_floridae_Unc4c KPRRMRVRTNFTSWQLEALERAFETTHYPDIFMREALALRLDLMESRVQV-WFQNRRAKWRKQE Ciona_intestinalis_118343665 KRKQRRYRTTFSAFQLEELERAFQKTHYPDVFTREELAMRVDLTEARVQV-WFQNRRAKWRKRE Ciona_intestinalis_Gsc AKRKRRHRTIFTEDQLEALENMFQKTHYPDVVMREQLAEKVELKEERVEV-WFKNRRAKWRKQK Ciona_intestinalis_OTX SRKQRRERTTFTRAQLDILEALFGKTRYPDIFMREEVALKINLPESRVQV-WFKNRRAKCRQQV Ciona_intestinalis_Otp VTKSKRHRTRFAPSQLSELERSFSSTHYPDIFMREEIAHRIGLTESRVQV-WFQNRRAKWKKRK Ciona_intestinalis_Pitx KRRQRRQRTHFTSQQLQELEALFARNRYPDMSTREEISAWTNLTEARVRV-WFKNRRAKWRKRE Cladonema_pacificum_ArxA PRKLRRSRTTFTTYQLHQLERAFDKTQYPDVFTREELAVRLDLSEARVQV-RIF----LLTPAQ Cladonema_pacificum_ArxB RRGHRRNRTTFTRQQLEELEKLFDSTHYPDVFAREELATRINLTEARVQV-RLFFSFCIRKICI Cladonema_pacificum_ArxC KRKQRRYRTTFTQFQLDELERAFDKTHYPDVFMREELAMRISLTEARVQV-RLCSNMVILQPCM Cladonema_pacificum_ArxD ----RRYRTTFTQLQLDELERAFEKTHYPDVFMREELAMRISLTEARVQV-------------- Cladonema_pacificum_Gsc STNKRRQRTIFTEHQLHVLEQMFSRTHYPDVLVREEIARVIGLTEEKVEV-SFVN--------- Cladonema_pacificum_Otp PSKQKRHRTRFSPAQLNELERYFSKTHYPDIFVREELAMRIGLTESRVQV-------------- Cladonema_pacificum_OtxA PRKQRRERTTFTKGQLEILENLFRETKYPDVFMREDVARRISLPESRVQV-RFHL--------- Cladonema_pacificum_OtxB ----RRERTTFTKSQLEILEDLFTKTHYPDIFMREEAARKINLPESRVQV-------------- Cladonema_pacificum_Pitx DHRIRRQRTHFTVTQLQKLEACFARNRYPDMAMREDIAQWCALSESRVRV-RKHIISQTHHQYS Danio_rerio_Alx1 SSKKRRHRTTFTSAQLEELEKVFQKTHYPDVYVREQLAMRTELTEARVQV-WFQNRRAKWRKRE 'Danio rerio Arx-like' KRKQRRYRTTFTSYQLEELERAFQKTHYPDVFTREELAMRLDLTEARVQV-WFQNRRAKWRKRE Danio_rerio_Dmbx1 QQKQRRSRTAFSVSQLQALEKAFQQTQYPDVGMRERLAVCINLPEARIQV-WFKNRRAKFRKGQ Danio_rerio_Gsc CRRKRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEV-WFKNRRAKWRRQK Danio_rerio_Mixer LFTHRRKRTNFTQQQIDVLEKVYLDTKYPDIYLREKLEALTGLPESRIQV-WFQNRRAKSRRQV Danio_rerio_OTX1b PRKQRRERTTFTRSQLDILEALFAKTRYPDIFMREEVALKINLPESRVQV-WFKNRRAKCRQQQ Danio_rerio_OtpB QQKQKRHRTRFTPAQLNELERSFAKTHYPDIFMREELALRIGLTESRVQV-WFQNRRAKWKKRK Danio_rerio_Otx2 PRKQRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQV-WFKNRRAKCRQQQ Danio_rerio_Pax3 KRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQV-WFSNRRARWRKQA Danio_rerio_Pax6 KRKLQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQV-WFSNRRAKWRREE Danio_rerio_Pitx2 KKRQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRV-WFKNRRAKWRKRE Danio_rerio_Pitx3 KKKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRV-WFKNRRAKWRKRE Danio_rerio_Rx1 KKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQV-WFQNRRAKWRRQE Danio_rerio_Uncx4.1 GCKRRRTRTNFTGWQLEELEKAFNESHYPDVFMREALALRLDLVESRVQV-WFQNRRAKWRKKE Drosophila_melanogaster_Alx KRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQV-WFQNRRAKWRKQE Drosophila_melanogaster_Eyegone EPKFRRNRTTFSPEQLEELEKEFDKSHYPCVSTRERLSSRTSLSEARVQV-WFSNRRAKWRRHQ Drosophila_melanogaster_Gooseberry KRKQRRSRTTFSNDQIDALERIFARTQYPDVYTREELAQSTGLTEARVQV-WFSNRRARLRKQL Drosophila_melanogaster_Gsc PKRKRRHRTIFTEEQLEQLEATFDKTHYPDVVLREQLALKVDLKEERVEV-WFKNRRAKWRKQK Drosophila_melanogaster_Otp QQDQKRHRTRFTPAQLNELERCFSKTHYPDIFMREEIAMRIGLTESRVQV-WFQNRRAKWKKRK Drosophila_melanogaster_Otx TRKQRRERTTFTRAQLDVLEALFGKTRYPDIFMREEVALKINLPESRVQV-WFKNRRAKCRQQL Drosophila_melanogaster_Ptx1 NKRQRRQRTHFTSQQLQELEHTSSRNRYPDMSTREEIAMWTNLTEARVRV-WFKNRRAKWRKRE Drosophila_melanogaster_Rx KKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQV-WFQNRRAKWRRQE Drosophila_melanogaster_Unc4 AAKRRRSRTNFNSWQLEELERAFSASHYPDIFMREALAMRLDLKESRVAV-WFQNRRAKVRKRE 'Hydra magnipapillata Arx-like' IENNKRNRTIFSKKQSCVLEDVFKKTHYPDLKCRYEISQQTKLAENRIQV-WFQNRRAKWRRTE Hydra_magnipapillata_Dmbx GRKHRRVRTAFTHHQLTTLERTFETSHYPDVVLRERLASFTGLAESRIQV-WFKNRRAKYRKHQ Hydra_magnipapillata_Gsc HFLKRRHRTIFSDEQLNVLERLFNKTHYPDVIVREEIAGIINLTEEKVEV-WFKNRRARWRKQK Hydra_magnipapillata_Otp HSKQKRHRTRFTQTQLNELERYFNKTHYPDIFVREELAMRIDLTESRVQV-WFQNRRAKWKKRR 'Hydra magnipapillata Otx1/2' PPKRRRERTTFTKAQLDVLEDMFGKTMYPDVFMREEVAKKINLAEARVQV-WFKNRRAKFRRSR Hydra_magnipapillata_OtxA PRKQRRERTTFTKFQLEILDNLFKETKYPDVFMREDVARRISLPESRVQV-WFKNRRAKHRQKS Hydra_magnipapillata_OtxB PRKQRRERTTFTKSQLEILEELFLKTHYPDIFMREEAARKINLPESRVQV-WFKNRRAKHRQKA Hydra_magnipapillata_Pitx DNRIRRQRTHFTVTQLHRLETCFARNRYPDMAMREDIAQWCSLTESRVRI-WFKNRRAKWRKKE Hydra_magnipapillata_Rx RQKLRRNRTTFTTYQLHQLERSFDKTQYPDVFTRENLALKLDLSEARVQV-WFQNRRAKWRKRE Hydra_magnipapillata_Unc4.1 ------MRTNFSPWQLEELETAFKKSYYPDVYTREVLALKLEIAESRIQV-WFQNRRAKWRKAE Lottia_gigantea_Dmbx1 HRKQRRSRTAFTNQQLAALEKTFGKTHYPDVVMRERLAMMTNLPEARIQV-WFKNRRAKFRKKQ Lottia_gigantea_Gsc QKRKRRHRTIFTEEQLEQLENTFHKTHYPDVLLREELALKVDLKEERVEV-WFKNRRAKWRKTK Lottia_gigantea_Otp PSKQKRHRTRFTPAQLNELERSFAKTHYPDIFMREEMALRIGLTESRVQV-WFQNRRAKWKKRK Lottia_gigantea_Otx PRKQRRERTTFTRAQLDVLESLFQKTRYPDIFMREEVALKINLPESRVQV-WFKNRRAKCRQQQ 'Lottia gigantea Pax3/7' TRKMRRNRTTFSGEQLEELEKVFEKTHYPDIYTREELAQRTKLTEARVQV-WFSNRRARWRKQV Lottia_gigantea_Pax6 RQKLRRNRTTFCQSQLEVLEQEFLKTHYPGVATREDLAVKTGLSEARVQV-WFSNRRAKWRRNE Lottia_gigantea_Pitx2 KKRQRRQRTHFTSQQLQELEATFARNRYPDMATREEISAWTNLTEARVRV-WFKNRRAKWRKRE Lottia_gigantea_Rx KKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAIKINLPEVRVQV-WFQNRRAKWRRQE Lottia_gigantea_Unc4.1 AAKRRRTRTNFTGWQLEELEKAFNDSHYPDVFMREALALKLDLVESRVQV-WFQNRRAKWRKKE Mnemiopsis_leidyi_PRD43 ---SRRFRTTFTSCQLQALEGAFQQTHYPDMYMREELAMRIDLTEARVQV-WFQNRRAKWRKRE Mnemiopsis_leidyi_PRD61 ---QRRNRTTFSSVQLHELERAFQQSHYPDVFTREELAMRLDLTEARVQV-WFQNRRAKWRKRE Mus_musculus_ALX1 SSKKRRHRTTFTSLQLEELEKVFQKTHYPDVYVREQLALRTELTEARVQV-WFQNRRAKWRKRE Mus_musculus_Dmbx1a HRKQRRSRTAFTAQQLEALEKTFQKTHYPDVVMRERLAMCTNLPEARVQV-WFKNRRAKFRKKQ Mus_musculus_Gsc CRRKRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEV-WFKNRRAKWRRQK Mus_musculus_MixerL1 SAPQRRKRTSFSSEQLQLLELVFRQTMYPDIHLRERLAALTLLPESRIQV-WFQNRRAKSRRQS Mus_musculus_OTP QQKQKRHRTRFTPAQLNELERSFAKTHYPDIFMREELALRIGLTESRVQV-WFQNRRAKWKKRK Mus_musculus_OTX1 PRKQRRERTTFTRSQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQV-WFKNRRAKCRQQQ Mus_musculus_Pax6 KRKLQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQV-WFSNRRAKWRREE Mus_musculus_Pax7 KRKQRRSRTTFTAEQLEELEKAFERTHYPDIYTREELAQRTKLTEARFQV-WFSNRRARWRKQA Mus_musculus_Pitx2 KKRQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRV-WFKNRRAKWRKRE Mus_musculus_Rx KKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAGKVNLPEVRVQV-WFQNRRAKWRRQE Mus_musculus_Uncx4.1 GCKRRRTRTNFTGWQLEELEKAFNESHYPDVFMREALALRLDLVESRVQV-WFQNRRAKWRKKE Nematostella_vectensis_Alx KRKKRRNRTTFTAYQLEEMERVFQKTHYPDVYTREQLALRCALTEARVQV-WFQNRRAKWRKRE Nematostella_vectensis_Arx KRKQRRYRTTFTSYQLEELERAFAKTHYPDVFTREALAVKIDLTEARVQV-WFQNRRAKWRKRE Nematostella_vectensis_DmbxA RAKHRRTRTAFTHQQLQILESTFSKTHYPDVVMREQLAAYINIPESRIQV-WFKNRRAKYRKQV Nematostella_vectensis_DmbxB RRGSRRTRTAFTHQQLTALEKVFSKTHYPDVEVREQLATSTNLQEARIQV-WFKNRRAKYRKDQ Nematostella_vectensis_DmbxC KKKPRRMRTCFTPYQLQVLENTFCNTHYPDVMLREQLASYVNLPEARIQV-WFKNRRAKHRKND Nematostella_vectensis_DmbxD GRKIRRTRTTFNQFQLDTLERAFSRTHYPDVLLREQLAVYTNLPESRIQV-WFKNRRAKYRKSK Nematostella_vectensis_Gsc PKRKRRHRTIFTEEQLELLETTFQKTHYPDVLLREELAMKVDLKEERVEV-WFKNRRAKWRKQK 'Nematostella vectensis Mixer-like' RADIKRKRRNLTKRQQKILETAYSTIKYPTIEDRQRLETSTQLSEDRIQV-WFQNRRAKDRRLQ Nematostella_vectensis_Otp AAKQKRHRTRFTPAQLNELERCFARTHYPDVFMREELAARIGLTESRVQV-WFQNRRAKWKKRK Nematostella_vectensis_OtxA TRKQRRERTTFTKNQLEVLEELFAKTRYPDIFMREEVAIKINLPESRVQV-WFKNRRAKTRQLE Nematostella_vectensis_OtxB PRKQRRERTTFTKNQLEILEELFAKTRYPDIFMREEVAIKINLPESRVQV-WFKNRRAKARQQA Nematostella_vectensis_OtxC PRKQRRERTTFTKNQLEILEELFAKTRYPDIFMREEVAIKINLPESRVQV-WFKNRRAKLRQLS Nematostella_vectensis_PaxB SKMSRRQRTNFTDEQIEKLEKVFEKTHYPDVFTREELAQQVNLSEARIQV-WYSNRRAKWRKEG Nematostella_vectensis_PaxC KRKLRRNRTTFTPDQLEMLEKEFEKSHYPDVATREELANKIDMSEARVQV-WFSNRRAKWRRHQ Nematostella_vectensis_PaxD CHKPRRSRTRFTVSQTDELERAFRKTHYPDIYAREELAQRLGLSEARVQV-WFSNRRARLRKER Nematostella_vectensis_PaxD2 TRKQRRSRTKFTSKQVDELEKAFLKTQYPDVYTREELAQRLNLTEARVQV-WFSNRRARLRKKK Nematostella_vectensis_Pitx KRKQRRQRTHFTSFQLQQLEGTFGRNRYPDMQMREEIALYTNLTEARVRV-WFKNRRAKWRKKE Nematostella_vectensis_Rx KKKLRRNRTTFTTFQLHELERAFEKSHYPDVYTREELALKISLPEVRVQV-WFQNKRAKWRREE Nematostella_vectensis_Unc4.1 LPKRRRSRTNFDSWQLEELEKIYHHNQYPDVFTREALALKLDLLESRIQV-WFQNRRAKMRREE Nematostella_vectensis_Unc4c ---RMRVRTNFSPWQLEELEHAFETTHYPDVFMREALAMRLDLTEARVQV-WFQNRRAKWRKRE 'Oscarella carmela Arx-likeA' PRKQRRYRTTFSPAQLQMLEDAFSKTHYPDVFTREELANRIGLAEARVQV-WFQNRRAKWRKRE 'Oscarella carmela Arx-likeB' KRKQRRNRTTFTAQQLEEMEKVFSRTHYPDVFTREELANRIGLTEARVQV-WFQNRRAKWRKRE 'Oscarella carmela Arx-likeC' KRKQRRYRTTFSSVQLEELEHAFEKTHYPDVFMREELALRINLTEARVQV-WFQNRRAKWRKKE Saccoglossus_kowalevskii_Alx KRKKRRNRTTFTSFQLDEMEKVFQRTHYPDVYSREQLALRCDLTEARVQV-WFQNRRAKWRKRE Saccoglossus_kowalevskii_Dmbx HRKQRRSRTAFTNQQLAALEKTFAKTHYPDVVMRERLAMCTNLPEARVQV-WFKNRRAKFRKQQ Saccoglossus_kowalevskii_Eyegone KKKSRRSRTTFSGDQLDVLEKEFDKTHYPCVNTREDLANKTHLSEARVQV-WFSNRRAKWRRHK Saccoglossus_kowalevskii_Otp PLKQKRHRTRFTPAQLNELERNFAKTHYPDIFMREEIAMRVGLTESRVQV-WFQNRRAKWKKRK Saccoglossus_kowalevskii_Otx PRKQRRERTTFTRAQLDILESLFGKTRYPDIFMREEVALKINLPESRVQV-WFKNRRAKCRQQE Saccoglossus_kowalevskii_Pax6 KRKLQRNRTSFTQYQIETLEKEFERTHYPDVFARERLAQKIDLPEARIQV-WFSNRRAKWRREE Saccoglossus_kowalevskii_Pitx2 NRRQRRQRTHFTSQQLQELEAHFARNRYPDMSTREEISAWTNLTEQRVRV-WFKNRRAKWRKRE Saccoglossus_kowalevskii_Rx KKKHRRNRTTFTTFQLHELERAFEKSHYPDVYSREELALKVNLPEVRVQV-WFQNRRAKWRRQE 'Saccoglossus kowalevskii Rx-like' G-KPKRSRTTFSSRQLQELERAFRRTHYPDMFTRERLARRIGLPESRVQV-WFQNRRAKWRKKE Saccoglossus_kowalevskii_Unc4.1 SGKRRRTRTNFNGWQLEELEKAFNDSHYPDVFTREALAMKLDLVESRVQV-WFQNRRAKWRKKE 'Saccoglossus kowalevskii Unc4c-like' KSRRMRVRTNFAAWQLDELERAFETTHYPDIFMREALAMRLDLMEARVQV-WFQNRRAKWRKRE Tribolium_castaneum_Alx KRKQRRYRTTFTSYQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQV-WFQNRRAKWRKQE Tribolium_castaneum_Gsc PKRKRRHRTIFSEEQLEQLEATFEQTHYPDVVLREQLALKVDLKEERVEV-WFKNRRAKWRKQK Tribolium_castaneum_Otx1 PRKQRRERTTFTRAQLDLLEGLFAKTRYPDIFMREEVAVKINLPESRVQV-WFKNRRAKCRQQL Tribolium_castaneum_Otx2 QRKQRRERTTFTRAQLDVLEALFGKTRYPDIFMREEVALKINLPESRVQV-WFKNRRAKCRQQQ Tribolium_castaneum_Pitx1 TKRQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEARVRV-WFKNRRAKWRKRE Tribolium_castaneum_Rx KKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQV-WFQNRRAKWRRQE Trichoplax_adhaerens_196002946 ---RKRYRTTFTSQQLEELERAFELAPYPDVFTREDLATKISLTEARVQV-WFQNRRAKWRKKE Trichoplax_adhaerens_Gsc ---KRRHRTIFTDEQIAELEKLYEQTQYPDVTMRERIAQKIDLKEERVEV-WFKNRRAKSRKER Trichoplax_adhaerens_Otp ---PKRHRTRFTPGQLSELERCFSKTHYPDIFMREELALRIGLSESRVQV-WFQNRRAKYKKKK Trichoplax_adhaerens_Pitx KRRPRRQRTHFTSYQLQELEAAFARNRYPDMTTREEIAMWINLNESRVRV-WFKNRRAKWRKRE Trichoplax_adhaerens_Rx ---LRRSRTTFTTLQLHQLERAFEKTQYPDVFSREDLAMRLELTEARVQV-WFQNRRAKWRKQE ; END; [ The following blocks are output data for analysis step 14285 ] BEGIN TREES; TITLE 'Results of the Prd/Pitx transcription factor gene superfamily'; LINK TAXA = TaxaForAnalysisStep14285; TREE BioNJ_consensus_tree = [&R] ('Acropora digitifera Mixer-like':0.03121,((((((Mus_musculus_Pax6:1.0E-5,Danio_rerio_Pax6:1.0E-5)98:1.0E-5,Branchiostoma_floridae_Pax6:1.0E-5)97:0.05885,Saccoglossus_kowalevskii_Pax6:1.0E-5)100:0.58064,(Tribolium_castaneum_Alx:1.0E-5,Drosophila_melanogaster_Alx:0.0178)97:0.14263,((Acropora_digitifera_Rx:1.0E-5,Acropora_millepora_Rx:1.0E-5)98:0.05472,((Tribolium_castaneum_Rx:1.0E-5,Mus_musculus_Rx:0.01808)51:1.0E-5,Danio_rerio_Rx1:1.0E-5,Lottia_gigantea_Rx:0.03503,Drosophila_melanogaster_Rx:1.0E-5,Branchiostoma_floridae_Rax:0.03474,Saccoglossus_kowalevskii_Rx:0.03527)63:0.07521,Nematostella_vectensis_Rx:0.09231)96:0.32306,(((Hydra_magnipapillata_Pitx:0.03691,Cladonema_pacificum_Pitx:0.49947)96:0.37943,(Acropora_digitifera_Pitx:1.0E-5,Acropora_millepora_Pitx:1.0E-5)81:0.10872)60:0.1217,((Saccoglossus_kowalevskii_Pitx2:0.05516,Ciona_intestinalis_Pitx:1.9E-4)68:0.03563,Lottia_gigantea_Pitx2:0.01714)48:0.03493,((Danio_rerio_Pitx2:1.0E-5,Mus_musculus_Pitx2:1.0E-5)78:1.0E-5,Danio_rerio_Pitx3:0.01629)47:0.03502,Tribolium_castaneum_Pitx1:0.01729,Drosophila_melanogaster_Ptx1:0.07263,Branchiostoma_floridae_Pitx2:0.09174,Trichoplax_adhaerens_Pitx:0.16291,Nematostella_vectensis_Pitx:0.23404)94:0.5577,((Lottia_gigantea_Dmbx1:0.05389,Saccoglossus_kowalevskii_Dmbx:0.01891)59:0.04194,Mus_musculus_Dmbx1a:0.02682,Branchiostoma_floridae_Dmbx:0.07927,Danio_rerio_Dmbx1:0.33912)82:0.51582,((Acropora_digitifera_Pax6a:1.0E-5,Acropora_millepora_Pax6a:1.0E-5)100:0.14292,Nematostella_vectensis_PaxB:0.1991)79:0.52127,((Acropora_digitifera_OtxA:1.0E-5,Acropora_millepora_OtxA:1.0E-5)98:0.05891,(Acropora_millepora_OtxB:1.0E-5,Acropora_digitifera_OtxB:1.0E-5)92:0.05522,(Hydra_magnipapillata_OtxA:0.0512,Cladonema_pacificum_OtxA:0.10816)85:0.23576,(Cladonema_pacificum_OtxB:0.02992,Hydra_magnipapillata_OtxB:0.02938)57:0.16086,((Danio_rerio_OTX1b:0.0186,Mus_musculus_OTX1:1.0E-5)57:0.01893,Danio_rerio_Otx2:1.0E-5,Tribolium_castaneum_Otx2:0.03878,Drosophila_melanogaster_Otx:0.06173,Branchiostoma_floridae_Otx:0.02008,Lottia_gigantea_Otx:0.03897,Ciona_intestinalis_OTX:0.08487,Saccoglossus_kowalevskii_Otx:0.07974,Tribolium_castaneum_Otx1:0.0837)54:0.14293,(Nematostella_vectensis_OtxB:0.02489,Nematostella_vectensis_OtxC:0.03513)50:0.07444,Acropora_digitifera_OtxC:0.03605,Nematostella_vectensis_OtxA:0.18031,Acropora_digitifera_OtxD:0.13647,'Hydra magnipapillata Otx1/2':0.39834)77:0.74827,((Acropora_digitifera_Arx:1.0E-5,Acropora_millepora_Arx:1.0E-5)96:0.04957,Nematostella_vectensis_Arx:0.01594)72:0.07418,((Tribolium_castaneum_Gsc:0.04204,Drosophila_melanogaster_Gsc:0.01034)91:0.09666,(Cladonema_pacificum_Gsc:0.4353,Hydra_magnipapillata_Gsc:0.18728)86:0.52011,((Acropora_digitifera_Gsc:1.0E-5,Acropora_millepora_Gsc:1.0E-5)100:0.07611,Nematostella_vectensis_Gsc:0.01114)82:0.02285,((Danio_rerio_Gsc:1.0E-5,Mus_musculus_Gsc:1.0E-5)100:0.31928,Ciona_intestinalis_Gsc:1.0E-5)52:0.18236,Lottia_gigantea_Gsc:0.08029,Branchiostoma_floridae_Gsc:0.10626,Trichoplax_adhaerens_Gsc:0.51477)70:0.60634,(((Acropora_digitifera_Otp:1.0E-5,Acropora_millepora_Otp:1.0E-5)100:0.47871,Cladonema_pacificum_Otp:0.09014)65:1.0E-5,(Danio_rerio_OtpB:1.0E-5,Mus_musculus_OTP:1.0E-5)63:0.09218,Lottia_gigantea_Otp:0.06853,Saccoglossus_kowalevskii_Otp:0.09552,Drosophila_melanogaster_Otp:0.0967,Trichoplax_adhaerens_Otp:0.18078,Ciona_intestinalis_Otp:0.25988,Nematostella_vectensis_Otp:0.11651,Hydra_magnipapillata_Otp:0.18266)67:0.46321,(Branchiostoma_floridae_Rx:0.10438,'Saccoglossus kowalevskii Rx-like':0.14948)65:0.35817,((Mus_musculus_ALX1:1.0E-5,Danio_rerio_Alx1:0.03611)98:0.14362,(((Acropora_digitifera_Alx:1.0E-5,Acropora_millepora_Alx:1.0E-5)91:0.01844,Nematostella_vectensis_Alx:0.05884,Saccoglossus_kowalevskii_Alx:0.07502)55:0.00889,'Branchiostoma floridae Alx-like':0.06726)79:0.04858)61:0.16254,(Hydra_magnipapillata_Rx:0.15544,Trichoplax_adhaerens_Rx:0.11402)59:0.23939,(((Acropora_digitifera_Unc4.1:1.0E-5,Acropora_millepora_Unc4.1:1.0E-5)78:0.07299,Nematostella_vectensis_Unc4.1:0.18851)97:0.34631,((Acropora_digitifera_Unc4c:1.0E-5,Acropora_millepora_Unc4c:1.0E-5)98:0.04281,Branchiostoma_floridae_Unc4c:0.17526,'Saccoglossus kowalevskii Unc4c-like':0.12768,Nematostella_vectensis_Unc4c:0.02724)85:0.18648,((((Danio_rerio_Uncx4.1:1.0E-5,Mus_musculus_Uncx4.1:1.0E-5)96:0.08306,Lottia_gigantea_Unc4.1:1.0E-5)48:0.04461,Saccoglossus_kowalevskii_Unc4.1:0.05745)67:0.12557,Branchiostoma_floridae_Unc4:0.04427,Drosophila_melanogaster_Unc4:0.20867)47:0.12826,Hydra_magnipapillata_Unc4.1:0.45238)58:0.25527,(('Acropora digitifera Pax3/7a':1.0E-5,'Acropora millepora Pax3/7a':1.0E-5)100:0.19914,(('Acropora digitifera Pax3/7b':1.0E-5,'Acropora millepora Pax3/7b':1.0E-5)95:0.07084,Nematostella_vectensis_PaxD:0.28644)72:0.13255,Nematostella_vectensis_PaxD2:0.04883,Drosophila_melanogaster_Gooseberry:0.41805)49:0.40752,(((Cladonema_pacificum_ArxC:0.02672,Cladonema_pacificum_ArxB:0.67701)72:1.0E-5,Cladonema_pacificum_ArxA:0.56595)64:0.042,Cladonema_pacificum_ArxD:0.02819)49:0.51636,((Acropora_digitifera_DmbxD:0.10736,Nematostella_vectensis_DmbxD:0.07003)95:0.29136,((Acropora_digitifera_DmbxB:1.0E-5,Acropora_millepora_DmbxB:1.0E-5)97:0.10686,Nematostella_vectensis_DmbxB:0.18617)69:0.23788,Nematostella_vectensis_DmbxA:0.23056,Nematostella_vectensis_DmbxC:0.40377,Hydra_magnipapillata_Dmbx:0.34077)48:0.81225,((Saccoglossus_kowalevskii_Eyegone:0.15332,Drosophila_melanogaster_Eyegone:0.26946)68:0.10484,Lottia_gigantea_Pax6:0.32715,Acropora_digitifera_Pax6b:0.21315,Nematostella_vectensis_PaxC:0.15395)47:0.50944,(((Danio_rerio_Pax3:0.03441,Mus_musculus_Pax7:0.01696)59:1.0E-5,'Branchiostoma floridae Pax3/7':0.03496)59:1.0E-5,'Lottia gigantea Pax3/7':0.15524)46:0.37005,'Oscarella carmela Arx-likeB':0.24914,'Danio rerio Arx-like':0.02106,Branchiostoma_floridae_Q50:0.03873,Mnemiopsis_leidyi_PRD61:0.17435,Ciona_intestinalis_118343665:0.07895,'Oscarella carmela Arx-likeA':0.34145,Trichoplax_adhaerens_196002946:0.32497,'Amphimedon queenslandica Arx-likeB':0.23256,'Oscarella carmela Arx-likeC':0.16138,Mnemiopsis_leidyi_PRD43:0.25629,'Amphimedon queenslandica Arx-likeA':0.27698,'Amphimedon queenslandica Arx-likeC':0.61873,Acropora_millepora_1217446:0.8598,'Hydra magnipapillata Arx-like':1.67117)52:1.42352,(Danio_rerio_Mixer:0.26881,Mus_musculus_MixerL1:0.48042)52:1.0E-5)100:1.00979,'Nematostella vectensis Mixer-like':0.39892)65:0.24625,'Acropora millepora Mixer-like':1.0E-5); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr76772] END; BEGIN TREES; TITLE 'Results of the Prd/Pitx transcription factor gene superfamily'; LINK TAXA = TaxaForAnalysisStep14285; TREE PhyML_ML_tree = [&R] (((((((((((Trichoplax_adhaerens_196002946:0.267028,((Nematostella_vectensis_Arx:0.02949,(Acropora_millepora_Arx:0.0,Acropora_digitifera_Arx:0.0)95:0.027426)66:0.03212,(('Oscarella carmela Arx-likeA':0.182072,'Oscarella carmela Arx-likeB':0.076275)30:0.050934,(Drosophila_melanogaster_Alx:0.015076,Tribolium_castaneum_Alx:1.0E-6)100:0.042859)18:0.04364)7:0.018259)2:0.007952,(((((((((((Branchiostoma_floridae_Gsc:0.083516,(Nematostella_vectensis_Gsc:0.0144,(Acropora_millepora_Gsc:0.0,Acropora_digitifera_Gsc:0.0)100:0.071801)53:2.0E-6)37:0.009957,((Drosophila_melanogaster_Gsc:6.98E-4,Tribolium_castaneum_Gsc:0.047434)99:0.078976,Lottia_gigantea_Gsc:0.048252)23:0.034483)51:0.039931,(((Mus_musculus_Gsc:0.0,Danio_rerio_Gsc:0.0)100:0.260558,Ciona_intestinalis_Gsc:0.040393)47:0.021839,((Hydra_magnipapillata_Gsc:0.152793,Cladonema_pacificum_Gsc:0.350111)95:0.319212,Trichoplax_adhaerens_Gsc:0.323896)21:0.078438)25:0.075598)81:0.263564,('Hydra magnipapillata Otx1/2':0.236325,((((((Acropora_millepora_OtxA:0.0,Acropora_digitifera_OtxA:0.0)100:0.033923,((Cladonema_pacificum_OtxA:0.091297,Hydra_magnipapillata_OtxA:0.035021)95:0.127798,(Hydra_magnipapillata_OtxB:0.035868,Cladonema_pacificum_OtxB:0.004484)72:0.052264)31:0.07442)11:0.006617,Acropora_digitifera_OtxC:0.023276)10:0.012534,(Acropora_digitifera_OtxD:0.080006,(Acropora_digitifera_OtxB:0.0,Acropora_millepora_OtxB:0.0)98:0.015501)58:0.028685)8:0.016626,(Nematostella_vectensis_OtxB:0.017005,(Nematostella_vectensis_OtxC:0.013767,Nematostella_vectensis_OtxA:0.063396)44:0.022301)64:0.051241)18:0.037721,(((Saccoglossus_kowalevskii_Otx:0.031719,Lottia_gigantea_Otx:0.016376)33:0.015183,((Ciona_intestinalis_OTX:0.047219,Drosophila_melanogaster_Otx:4.0E-6)45:0.031689,Tribolium_castaneum_Otx2:3.2E-5)47:0.016357)12:0.014827,(Tribolium_castaneum_Otx1:0.069227,((Branchiostoma_floridae_Otx:0.01545,Danio_rerio_Otx2:1.0E-6)35:1.0E-6,(Mus_musculus_OTX1:1.0E-6,Danio_rerio_OTX1b:0.014787)47:0.014979)21:1.0E-6)15:2.0E-6)62:0.057824)43:0.077438)82:0.253665)20:0.071046,(Branchiostoma_floridae_Dmbx:0.041145,(((Lottia_gigantea_Dmbx1:0.037152,((((Hydra_magnipapillata_Dmbx:0.20308,(Nematostella_vectensis_DmbxD:0.055202,Acropora_digitifera_DmbxD:0.087669)98:0.224451)47:0.043112,Nematostella_vectensis_DmbxC:0.35432)20:0.030694,(Nematostella_vectensis_DmbxB:0.120415,(Acropora_millepora_DmbxB:0.0,Acropora_digitifera_DmbxB:0.0)100:0.13188)82:0.141381)20:0.014047,Nematostella_vectensis_DmbxA:0.12533)42:0.207377)5:0.021828,Saccoglossus_kowalevskii_Dmbx:4.0E-6)5:0.036186,(Danio_rerio_Dmbx1:0.271999,Mus_musculus_Dmbx1a:2.0E-6)49:0.03572)10:0.021366)34:0.149707)11:0.083072,((((Nematostella_vectensis_PaxB:0.20718,(Acropora_millepora_Pax6a:0.0,Acropora_digitifera_Pax6a:0.0)100:0.113099)90:0.171732,(Saccoglossus_kowalevskii_Pax6:0.027606,(Branchiostoma_floridae_Pax6:0.0,(Danio_rerio_Pax6:0.0,Mus_musculus_Pax6:0.0)38:0.0)98:0.024806)98:0.203706)35:0.093664,(Nematostella_vectensis_PaxC:0.112897,((Lottia_gigantea_Pax6:0.284253,(Drosophila_melanogaster_Eyegone:0.22613,Saccoglossus_kowalevskii_Eyegone:0.161215)67:0.068159)22:0.020804,Acropora_digitifera_Pax6b:0.142309)61:0.058474)69:0.094603)25:0.106428,(((('Acropora millepora Pax3/7a':0.0,'Acropora digitifera Pax3/7a':0.0)100:0.145055,(Nematostella_vectensis_PaxD2:0.02033,(Nematostella_vectensis_PaxD:0.237206,('Acropora millepora Pax3/7b':0.0,'Acropora digitifera Pax3/7b':0.0)100:0.083922)88:0.127258)49:0.040325)60:0.114191,Drosophila_melanogaster_Gooseberry:0.224276)40:0.059564,('Branchiostoma floridae Pax3/7':0.010348,('Lottia gigantea Pax3/7':0.135976,(Mus_musculus_Pax7:0.015545,Danio_rerio_Pax3:0.031294)65:2.0E-6)31:0.024387)54:0.061497)40:0.054754)16:0.05336)0:0.062997,((Nematostella_vectensis_Pitx:0.110896,((Cladonema_pacificum_Pitx:0.422247,Hydra_magnipapillata_Pitx:0.0)97:0.377123,(Acropora_millepora_Pitx:0.0,Acropora_digitifera_Pitx:0.0)99:0.058411)33:0.034913)23:0.0475,(Trichoplax_adhaerens_Pitx:0.099812,((Branchiostoma_floridae_Pitx2:0.035165,((Ciona_intestinalis_Pitx:0.006972,Saccoglossus_kowalevskii_Pitx2:0.04406)82:0.022154,Lottia_gigantea_Pitx2:0.019385)48:0.015515)57:0.018022,((Danio_rerio_Pitx3:0.014253,(Mus_musculus_Pitx2:0.0,Danio_rerio_Pitx2:0.0)66:1.0E-6)74:0.031159,(Drosophila_melanogaster_Ptx1:0.059471,Tribolium_castaneum_Pitx1:0.008239)58:0.007951)35:0.020925)56:0.018993)35:0.011593)94:0.311099)1:0.032897,((Danio_rerio_Alx1:0.030796,Mus_musculus_ALX1:6.0E-6)96:0.126487,('Branchiostoma floridae Alx-like':0.064729,((Saccoglossus_kowalevskii_Alx:0.064663,(Acropora_millepora_Alx:0.0,Acropora_digitifera_Alx:0.0)98:0.015655)37:2.0E-6,Nematostella_vectensis_Alx:0.051199)46:1.2E-5)71:0.036569)73:0.094436)0:0.02094,(((((Hydra_magnipapillata_Unc4.1:0.358192,(Branchiostoma_floridae_Unc4:1.3E-5,(Drosophila_melanogaster_Unc4:0.165442,(((Mus_musculus_Uncx4.1:0.0,Danio_rerio_Uncx4.1:0.0)100:0.070046,Lottia_gigantea_Unc4.1:3.0E-6)39:0.024814,Saccoglossus_kowalevskii_Unc4.1:0.061444)77:0.06915)44:0.063643)56:0.051918)21:0.025409,(Nematostella_vectensis_Unc4.1:0.159175,(Acropora_millepora_Unc4.1:0.0,Acropora_digitifera_Unc4.1:0.0)100:0.064372)98:0.255127)32:0.087701,((Nematostella_vectensis_Unc4c:0.019753,(Acropora_millepora_Unc4c:0.0,Acropora_digitifera_Unc4c:0.0)100:0.033241)68:0.019989,('Saccoglossus kowalevskii Unc4c-like':0.062377,Branchiostoma_floridae_Unc4c:0.08452)68:0.039239)90:0.112179)44:0.135402,Acropora_millepora_1217446:0.635317)26:7.0E-6,((((Nematostella_vectensis_Rx:0.072674,(Acropora_millepora_Rx:0.0,Acropora_digitifera_Rx:0.0)99:0.043701)42:0.009849,((Saccoglossus_kowalevskii_Rx:0.015652,(Drosophila_melanogaster_Rx:0.0,(Danio_rerio_Rx1:0.0,(Mus_musculus_Rx:0.016349,Tribolium_castaneum_Rx:0.0)4:1.0E-6)10:2.0E-6)47:0.015114)51:0.015209,(Branchiostoma_floridae_Rax:1.0E-6,Lottia_gigantea_Rx:0.031063)30:2.0E-6)61:0.026678)96:0.211429,Mnemiopsis_leidyi_PRD61:0.054367)11:0.020516,(Trichoplax_adhaerens_Rx:0.107946,Hydra_magnipapillata_Rx:0.119012)56:0.121379)7:0.02241)0:2.0E-6)0:0.016027,'Danio rerio Arx-like':1.0E-6)0:0.015411,(Branchiostoma_floridae_Q50:0.016337,Ciona_intestinalis_118343665:0.047501)32:0.015014)0:2.0E-6)0:0.01757,('Oscarella carmela Arx-likeC':0.08191,((((Cladonema_pacificum_ArxC:3.0E-6,(Cladonema_pacificum_ArxA:0.382978,Cladonema_pacificum_ArxB:0.447703)32:0.105642)32:0.05421,Cladonema_pacificum_ArxD:0.018655)58:0.310222,'Amphimedon queenslandica Arx-likeA':0.157597)7:4.0E-6,'Amphimedon queenslandica Arx-likeB':0.133606)6:0.016267)3:0.035541)0:2.7E-5,Mnemiopsis_leidyi_PRD43:0.18115)5:0.140847,(Hydra_magnipapillata_Otp:0.130286,(((((Acropora_millepora_Otp:2.0E-6,Acropora_digitifera_Otp:0.0)100:0.386119,Cladonema_pacificum_Otp:0.060014)14:2.0E-6,(Drosophila_melanogaster_Otp:0.039385,Saccoglossus_kowalevskii_Otp:0.069277)20:0.027171)0:2.0E-6,(Nematostella_vectensis_Otp:0.087079,((Mus_musculus_OTP:0.0,Danio_rerio_OtpB:0.0)85:0.032563,Lottia_gigantea_Otp:0.017616)36:0.031996)1:0.016602)8:3.0E-6,(Ciona_intestinalis_Otp:0.167707,Trichoplax_adhaerens_Otp:0.11215)37:0.032488)30:0.014628)89:0.202143)8:0.105269,(('Hydra magnipapillata Arx-like':1.063773,Branchiostoma_floridae_Rx:6.0E-6)5:0.049876,'Saccoglossus kowalevskii Rx-like':0.154582)6:0.100119)6:0.2406,'Amphimedon queenslandica Arx-likeC':0.028876)72:0.676698,Mus_musculus_MixerL1:0.309597)71:0.281768,Danio_rerio_Mixer:0.060416)100:1.05579,'Nematostella vectensis Mixer-like':0.373721)92:0.227873,'Acropora millepora Mixer-like':2.2E-5,'Acropora digitifera Mixer-like':0.028045); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr76770] END; BEGIN TREES; TITLE 'Results of the Prd/Pitx transcription factor gene superfamily'; LINK TAXA = TaxaForAnalysisStep14285; TREE IQPNNI_ML_consensus_tree = [&R] ('Acropora digitifera Mixer-like':0.03151,((((((Mus_musculus_Pax6:1.0E-5,Danio_rerio_Pax6:1.0E-5,Branchiostoma_floridae_Pax6:1.0E-5)85:0.05952,Saccoglossus_kowalevskii_Pax6:1.0E-5)96:0.52719,(((Acropora_digitifera_Pitx:1.0E-5,Acropora_millepora_Pitx:1.0E-5)100:0.05658,(Hydra_magnipapillata_Pitx:0.0322,Cladonema_pacificum_Pitx:0.51581)97:0.42579)54:0.10638,(((Danio_rerio_Pitx2:1.0E-5,Mus_musculus_Pitx2:1.0E-5)72:1.0E-5,Danio_rerio_Pitx3:0.01645)71:0.03535,(Tribolium_castaneum_Pitx1:0.01567,Drosophila_melanogaster_Ptx1:0.07261)66:0.00248,(((Saccoglossus_kowalevskii_Pitx2:0.05582,Ciona_intestinalis_Pitx:1.0E-5)77:0.05533,Lottia_gigantea_Pitx2:1.0E-5)48:0.01799,Branchiostoma_floridae_Pitx2:0.05378)40:0.03547)49:0.05739,Trichoplax_adhaerens_Pitx:0.13043,Nematostella_vectensis_Pitx:0.19319)96:0.44784,(Tribolium_castaneum_Alx:1.0E-5,Drosophila_melanogaster_Alx:0.01794)93:0.16691,((((Tribolium_castaneum_Rx:1.0E-5,Danio_rerio_Rx1:1.0E-5,Drosophila_melanogaster_Rx:1.0E-5)55:1.0E-5,Mus_musculus_Rx:0.01828,Lottia_gigantea_Rx:0.03538)41:0.03509,Branchiostoma_floridae_Rax:1.0E-5,Saccoglossus_kowalevskii_Rx:0.03574)52:0.0299,((Acropora_digitifera_Rx:1.0E-5,Acropora_millepora_Rx:1.0E-5)98:0.04608,Nematostella_vectensis_Rx:0.08129)41:0.01776)89:0.2854,((Acropora_digitifera_Pax6a:1.0E-5,Acropora_millepora_Pax6a:1.0E-5)100:0.1432,Nematostella_vectensis_PaxB:0.20309)79:0.49888,((Acropora_digitifera_OtxA:1.0E-5,Acropora_millepora_OtxA:1.0E-5)100:0.05953,(Hydra_magnipapillata_OtxA:0.05211,Cladonema_pacificum_OtxA:0.10941)86:0.24125,(Cladonema_pacificum_OtxB:0.03,Hydra_magnipapillata_OtxB:0.03012)76:0.16393,((Nematostella_vectensis_OtxC:0.01528,Nematostella_vectensis_OtxA:0.07805)52:0.02581,Nematostella_vectensis_OtxB:0.0214)52:0.07852,((Acropora_millepora_OtxB:1.0E-5,Acropora_digitifera_OtxB:1.0E-5)99:0.01924,Acropora_digitifera_OtxD:0.09829)51:0.03665,((Danio_rerio_OTX1b:0.01894,Mus_musculus_OTX1:1.0E-5)44:0.01928,(Drosophila_melanogaster_Otx:1.0E-5,Ciona_intestinalis_OTX:0.06156)39:0.06264,Danio_rerio_Otx2:1.0E-5,Tribolium_castaneum_Otx2:0.03952,Branchiostoma_floridae_Otx:0.02033,Lottia_gigantea_Otx:0.03971,Saccoglossus_kowalevskii_Otx:0.08109,Tribolium_castaneum_Otx1:0.08495)49:0.14502,Acropora_digitifera_OtxC:0.03636,'Hydra magnipapillata Otx1/2':0.40462)78:0.74392,((Danio_rerio_Gsc:1.0E-5,Mus_musculus_Gsc:1.0E-5)100:0.28358,(Cladonema_pacificum_Gsc:0.44299,Hydra_magnipapillata_Gsc:0.18611)84:0.45566,((Acropora_digitifera_Gsc:1.0E-5,Acropora_millepora_Gsc:1.0E-5)100:0.07643,(Tribolium_castaneum_Gsc:0.04362,Drosophila_melanogaster_Gsc:0.00924)89:0.12055,Nematostella_vectensis_Gsc:0.01683,Lottia_gigantea_Gsc:0.09816,Branchiostoma_floridae_Gsc:0.0958)39:0.14011,Ciona_intestinalis_Gsc:0.0681,Trichoplax_adhaerens_Gsc:0.42158)70:0.71452,((Danio_rerio_OtpB:1.0E-5,Mus_musculus_OTP:1.0E-5)96:0.07961,((Acropora_digitifera_Otp:1.0E-5,Acropora_millepora_Otp:1.0E-5)100:0.33109,Nematostella_vectensis_Otp:1.0E-5)86:0.12556,(Cladonema_pacificum_Otp:0.02368,Hydra_magnipapillata_Otp:0.12303)67:0.06641,Lottia_gigantea_Otp:0.05854,Saccoglossus_kowalevskii_Otp:0.0924,Drosophila_melanogaster_Otp:0.10945,Trichoplax_adhaerens_Otp:0.19898,Ciona_intestinalis_Otp:0.25349)67:0.46248,(((Acropora_digitifera_Unc4.1:1.0E-5,Acropora_millepora_Unc4.1:1.0E-5)100:0.10981,Nematostella_vectensis_Unc4.1:0.16464)95:0.38197,((Branchiostoma_floridae_Unc4c:0.0986,'Saccoglossus kowalevskii Unc4c-like':0.08449)56:0.03783,((Acropora_digitifera_Unc4c:1.0E-5,Acropora_millepora_Unc4c:1.0E-5)100:0.04141,Nematostella_vectensis_Unc4c:0.02438)53:0.04528)78:0.25223,(((Danio_rerio_Uncx4.1:1.0E-5,Mus_musculus_Uncx4.1:1.0E-5)98:0.08409,Lottia_gigantea_Unc4.1:1.0E-5)46:0.04517,Saccoglossus_kowalevskii_Unc4.1:0.0579)55:0.13162,Branchiostoma_floridae_Unc4:0.04904,Drosophila_melanogaster_Unc4:0.21594,Hydra_magnipapillata_Unc4.1:0.51145)63:0.38165,(((Saccoglossus_kowalevskii_Eyegone:0.14184,Drosophila_melanogaster_Eyegone:0.28164)60:0.09236,Lottia_gigantea_Pax6:0.33671,Acropora_digitifera_Pax6b:0.20728)51:0.11401,Nematostella_vectensis_PaxC:0.07254)61:0.37763,((Acropora_digitifera_DmbxB:1.0E-5,Acropora_millepora_DmbxB:1.0E-5)100:0.19422,Nematostella_vectensis_DmbxB:0.09254)61:0.89791,((Acropora_digitifera_Arx:1.0E-5,Acropora_millepora_Arx:1.0E-5)96:0.05355,Nematostella_vectensis_Arx:0.0109)59:0.09739,((Mus_musculus_ALX1:1.0E-5,Danio_rerio_Alx1:0.03646)89:0.15982,((Acropora_digitifera_Alx:1.0E-5,Acropora_millepora_Alx:1.0E-5)99:0.01863,Nematostella_vectensis_Alx:0.05936,Saccoglossus_kowalevskii_Alx:0.0758,'Branchiostoma floridae Alx-like':0.07454)53:0.03725)55:0.15228,(Branchiostoma_floridae_Rx:0.09417,'Saccoglossus kowalevskii Rx-like':0.16319)52:0.33606,((Mus_musculus_Dmbx1a:1.0E-5,Danio_rerio_Dmbx1:0.32541)41:0.03728,Lottia_gigantea_Dmbx1:0.05893,Saccoglossus_kowalevskii_Dmbx:0.03829,Branchiostoma_floridae_Dmbx:0.08816)51:0.57431,((Danio_rerio_Pax3:0.03476,Mus_musculus_Pax7:0.01714)77:1.0E-5,'Branchiostoma floridae Pax3/7':0.03526,'Lottia gigantea Pax3/7':0.15689)44:0.35711,((Acropora_digitifera_DmbxD:0.17749,Nematostella_vectensis_DmbxD:1.0E-5)97:0.16314,Hydra_magnipapillata_Dmbx:0.51785)44:0.72819,((Cladonema_pacificum_ArxC:0.02702,Cladonema_pacificum_ArxD:0.04952,Cladonema_pacificum_ArxB:0.68296)62:0.24749,Cladonema_pacificum_ArxA:0.35061)42:0.36396,(('Acropora digitifera Pax3/7a':1.0E-5,'Acropora millepora Pax3/7a':1.0E-5)100:0.20106,(('Acropora digitifera Pax3/7b':1.0E-5,'Acropora millepora Pax3/7b':1.0E-5)100:0.07168,Nematostella_vectensis_PaxD:0.29155)79:0.12497,Nematostella_vectensis_PaxD2:0.05952)41:0.38538,'Oscarella carmela Arx-likeB':0.22399,'Danio rerio Arx-like':0.04862,Branchiostoma_floridae_Q50:0.05813,Mnemiopsis_leidyi_PRD61:0.16392,Ciona_intestinalis_118343665:0.10972,'Oscarella carmela Arx-likeA':0.38162,Trichoplax_adhaerens_196002946:0.34955,'Amphimedon queenslandica Arx-likeB':0.22453,'Oscarella carmela Arx-likeC':0.17542,Mnemiopsis_leidyi_PRD43:0.28418,'Amphimedon queenslandica Arx-likeA':0.28723,'Amphimedon queenslandica Arx-likeC':0.5819,Hydra_magnipapillata_Rx:0.33957,Trichoplax_adhaerens_Rx:0.3339,Acropora_millepora_1217446:0.79328,Drosophila_melanogaster_Gooseberry:0.68801,Nematostella_vectensis_DmbxA:0.96893,Nematostella_vectensis_DmbxC:0.9325,'Hydra magnipapillata Arx-like':1.53244)58:1.26833,Mus_musculus_MixerL1:0.23273)58:0.3841,Danio_rerio_Mixer:0.14058)99:1.05741,'Nematostella vectensis Mixer-like':0.39233)86:0.25938,'Acropora millepora Mixer-like':1.0E-5); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr76771] END;