#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; 0:31 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 14283 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep14283;
        DIMENSIONS NTAX=80;
        TAXLABELS
            Acropora_digitifera_Islet
            'Acropora digitifera Lhx1/5'
            'Acropora digitifera Lhx6/8'
            Acropora_digitifera_Lmx1
            'Acropora millepora Lhx1/5'
            'Amphimedon queenslandica Lhx1/5'
            'Amphimedon queenslandica Lhx3/4'
            Branchiostoma_floridae_Islet1
            'Branchiostoma floridae Lhx1/5'
            'Branchiostoma floridae Lhx2/9'
            'Branchiostoma floridae Lhx3/4'
            'Branchiostoma floridae Lhx6/8'
            Ciona_intestinalis_Islet1
            'Ciona intestinalis Lhx1/5'
            'Ciona intestinalis Lhx3/4'
            'Cladonema pacificum Lhx6/8'
            Danio_rerio_Islet
            Danio_rerio_Lhx1
            Danio_rerio_Lhx2
            Danio_rerio_Lhx3
            Danio_rerio_Lhx4
            Danio_rerio_Lhx5
            Danio_rerio_Lhx6
            Danio_rerio_Lhx8
            Danio_rerio_Lmx1b2
            Drosophila_melanogaster_Apterus
            Drosophila_melanogaster_Arrowhead
            'Drosophila melanogaster Lhx1/5'
            'Drosophila melanogaster Lhx3/4'
            Drosophila_melanogaster_Lmx1a
            Drosophila_melanogaster_Lmx1b
            Drosophila_melanogaster_Tailup
            'Hydra magnipapillata Lhx1/5'
            'Hydra magnipapillata Lhx6/8a'
            'Hydra magnipapillata Lhx6/8b'
            Hydra_magnipapillata_Lmx1
            Lottia_gigantea_Islet1
            'Lottia gigantea Lhx1/5'
            'Lottia gigantea Lhx2/9'
            'Lottia gigantea Lhx3/4'
            'Lottia gigantea Lhx6/8'
            Lottia_gigantea_Lmx1
            Mnemiopsis_leidyi_Islet
            'Mnemiopsis leidyi Lhx1/5'
            'Mnemiopsis leidyi Lhx3/4'
            Mnemiopsis_leidyi_Lmx1
            Mus_musculus_Islet1
            Mus_musculus_Lhx1
            Mus_musculus_Lhx2
            Mus_musculus_Lhx3
            Mus_musculus_Lhx4
            Mus_musculus_Lhx5
            Mus_musculus_Lhx6
            Mus_musculus_Lhx8
            Mus_musculus_Lhx9
            Mus_musculus_Lmo4
            Mus_musculus_Lmx1a
            Nematostella_vectensis_Islet
            'Nematostella vectensis Lhx1/5'
            'Nematostella vectensis Lhx2/9'
            'Nematostella vectensis Lhx3/4-like'
            'Nematostella vectensis Lhx6/8'
            Nematostella_vectensis_Lmo4
            Nematostella_vectensis_Lmx1
            Saccoglossus_kowalevskii_Islet1
            'Saccoglossus kowalevskii Lhx1/5'
            'Saccoglossus kowalevskii Lhx2/9'
            'Saccoglossus kowalevskii Lhx3/4'
            'Saccoglossus kowalevskii Lhx6/8'
            Saccoglossus_kowalevskii_Lmo4
            Saccoglossus_kowalevskii_Lmx1
            Tribolium_castaneum_Arrowhead
            'Tribolium castaneum Lhx1/5'
            'Tribolium castaneum Lhx3/4'
            Tribolium_castaneum_Lmx1a
            Tribolium_castaneum_Lmx1b
            Trichoplax_adhaerens_Islet
            'Trichoplax adhaerens Lhx1/5a'
            'Trichoplax adhaerens Lhx1/5b'
            'Trichoplax adhaerens Lhx2/9'
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M23499]

	TITLE 'LhX/Lim transcription factor gene family alignment';
	LINK TAXA = TaxaForAnalysisStep14283;
	DIMENSIONS NCHAR=201;
	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 ]
[                                               .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         . ]
Acropora_digitifera_Islet              CVGCGSQI--QDQYIL--RVAPDLEWHAGCL-KCADCHTYLDET-CTCFVRDGKTYCKRDYVRLFGT-K---CAKCSRSVTKNDFVMRAK--NQ-IYHIECFRCLACSRQLVPGDEYVLREPDGLFC-KEDNEIVER--SEKTTRVRTVLNEKQLHTLRTCYAANPRPDAMMKEQLVEMTGLSPRVIRVWFQNKRCKDKKK
'Acropora digitifera Lhx1/5'           CAGCELPIS--DKFLL--KVLDR-LWHIKCV-HCHDCKSALTN---KCYSREGKLFCKNDFYRRYGT-K---CAGCCLGISPNDMVRRAK--HL-VFHVKCFNCSTCNRQILTGDELYYVGDSKFVC-KEDYYQSRL--GTKRRGPRTTIKAKQLEALKATFAATPKPSRNIREKLAQETGLNMRVIQVWFQNRRSKERRL
'Acropora digitifera Lhx6/8'           CAGCKGRI--MDRYLV--KVSGK-AWHTSCL-KCCMCGLELGKE-ATCYTKEDRIYCKTDYARQFGT-K---CARCGRSIHANDWVRRAR--SS-VYHLACFACDACKRQLSTGEEFALKE-GHVLC-KLHYMESLD--CHKTKRVRTTFTEEQLQILQANFNVDSNPDGQDLERIAQLTGLSKRVTQVWFQNSRARQKKY
Acropora_digitifera_Lmx1               ---------------M--KVM-EEPWHENCL-QCCICRITLSRS---CFSKDRKLYCRNDYEKMYAT-K---CTGCKATIPANEFVMR-A-LGN-VYHLQCFVCAMCGQRLVKGQEFALKD-NKLYC-KEDYGKLPT--KKGPKRPRTILTSQQRKIFKSAFEISSKPCRKVREELSRETGLSVRVVQVWFQNQRAKIKKL
'Acropora millepora Lhx1/5'            CAGCELPIS--DKFLL--KVLDR-LWHIKCV-HCHDCKSALTN---KCFSREGKLFCKNDFYRRYGT-K---CAGCCLGISPNDMVRRAK--HL-VFHVKCFNCSTCNRQILTGDELYYVGDSKFVC-KEDYYQSRL--GTKRRGPRTTIKAKQLEALKATFAATPKPSRNIREKLAQETGLNMRVIQVWFQNRRSKERRL
'Amphimedon queenslandica Lhx1/5'      CAGCSEPIM--ERFLM--KVLDK-SWHVQCV-KCSDCQCLLSE---KCFSRDNKLYCRSDFFRQYGT-Q---CASCKEGLCPEDLVRRGV--NK-IYHVQCFKCSVCQRQLNTGEQLYLVQGEKFLC-DSCYPAPAP--DNRKGKTRTSINPKQLIVLQATYEKEPRPSRAMREDLAAQTGLTAKVIQVWFQNRRSKDKKD
'Amphimedon queenslandica Lhx3/4'      CAGCNTRI--FDRFIL--RVQDK-SWHAKCL-RCSDCQCQLSD---KCYSRSGQVYCKDDFSKRFGT-R---CAGCQQPIPPTQVVRRAQ--EN-VYHLQCFACFICQRQLSTGDEFYLMDDRKLVC-KADYEAAKA--DGSQKRPRTTISQKQLDLLKTAYCVSPKPSRHVRQELSDKTGLDMRVVQVWFQNKRAKDKRT
Branchiostoma_floridae_Islet1          CVGCGSHI--HDQYIL--RVAPDLEWHAACL-KCSDCNQYLDET-CTCFVREGKTYCKRCYVRLFGT-K---CAKCSLGFTKNDFVMRAK--NK-IYHIDCFRCVACSRQLIPGDEFALRE-DGLFC-KADHEVLER--GHKPTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKK
'Branchiostoma floridae Lhx1/5'        CAGCERPVL--DRFLL--NVLDR-AWHAKCV-RCSDCSCRLTE---KCFTRDSKLYCREDFFRRFGT-K---CAGCTQGILPNDLVRRAR--NK-VFHLKCFTCAACAKQMATGEELFVVDDDKFIC-KDCYHNNKV--GAKRRGPRTTIKAKQLETLKAAFAATPKPTRHIREQLAQETGLNMRVIQVWFQNRRSKERRM
'Branchiostoma floridae Lhx2/9'        CGGCGEKI--QDRFFL--HAVDR-QWHSACL-KCCECDVRLDCE-LTCFSKDGRIYCREDYYRRFAVQR---CGRCHLGITAREMVMRAR--DS-VYHLACFTCVTCDKALTTGDEFGMQG-SAIYC-RYHYETFMR--ATKTKRIRTSFKHHQLRTLKSYFAINHNPDSKDLQQLAQKTGLTKRVLQVWFQNARAKHRRN
'Branchiostoma floridae Lhx3/4'        CAGCEQVI--LDRFIL--KVLDR-SWHAKCL-QCSDCQAQLTD---KCFSRDGHVYCKDDFFRRFGT-K---CAGCGQGIPPTQVVRRAQ--DK-IYHLQCFACIMCKRQLATGDEFYLMEDAKLVC-KSDYEAAKQ--EGTQKRPRTTITAKQLETLKQAYQNSPKPARHVREQLSQETGLDMRVVQVWFQNRRAKEKRL
'Branchiostoma floridae Lhx6/8'        CTGCGGPI--QDKFLL--KVGER-QWHVKCL-RCSVCQTPLGRH-TTCYTREADVFCKADYIRQFGT-K---CAKCCRNIQSNDWVRRAK--TH-VYHLACFACDACKRQLSTGEEFALHD-GKVLC-KSHYLEAMD--GHRPKRVRTTFTEEQLRVLQANFNIDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKY
Ciona_intestinalis_Islet1              CVGCGSPI--HDQYIL--RVAPNLEWHAGCL-KCADCGQYLDET-CTCFVRDGKTYCKRDYTRLFGT-K---CNKCGLCFSKNDFVMRAR--DK-IYHIQCFKCVACSRQLIPGDEFALRD-DGLFC-KADHEVATS--DAKTTRVRTVLNEKQLHTLRTCYAANCRPDALMKEQLTEMTGLSSRVIRVWFQNKRCKDKKR
'Ciona intestinalis Lhx1/5'            CSRCNHVIS--NKFVF--QVDGK-FWHGDCV-VCSDCECPLSN---RCYVRNEELFCSDDFCRRFGK-K---CGGCGGALYPNDLVHKVGQINS-VFHVRCFVCYVCNNNLEPGKPFQANERGLLYS-EEEVWGESN--ATKRRGPRTTIKAKQLETLKNAFLSTPKPTRHIREKLAQDTGLSMRVIQVWFQNRRSKERRI
'Ciona intestinalis Lhx3/4'            CTGCDHHI--FDRYIL--KVQDK-PWHSQCL-KCNDCGRQLTD---KCFSRGSYVYCKEDFFKRFGT-K---CSGCELAIPPTQVVRRAQ--DN-VYHLECFRCFMCSEQLGTGDQFYLLDDSRLVC-KKDYEHAKS--DNGIKRPRTTITAKQLETLKIAYNQSPKPARHVREQLSSDTGLDMRVVQVWFQNRRAKEKRL
'Cladonema pacificum Lhx6/8'           --------------------------------------------------------------------K---CYSCQRAIQSTDWIRKAK--QN-VYHLACFACDICKRQLSTGEEFALLE-NSILC-KLHYVNQLE--TGKHKRVRTSFSEEQVQVLQANFEIDANPDSAELERIASDVSLPKRVTQVWFQNSRARQKKQ
Danio_rerio_Islet                      CVGCGNQI--HDQYIL--RVSPDLEWHAACL-KCAECNQYLDES-CTCFVRDGKTYCKRDYIRLYGI-K---CAKCNIGFSKNDFVMRAR--SK-VYHIECFRCVACSRQLIPGDEFALRE-DGLFC-RADHDVVER--PEKTTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR
Danio_rerio_Lhx1                       CAGCERPIL--DRFLL--NVLDR-AWHIKCV-QCCECKCNLTE---KCFSREGKLYCKNDFFRRFGT-K---CAGCAQGISPNDLVRRAR--SK-VFHLNCFTCMMCNKQLSTGEELYIIDENKFVC-KDDYLSN-T--GGKRRGPRTTIKAKQLETLKAAFAATPKPTRHIREQLAQETGLNMRVIQVWFQNRRSKERRM
Danio_rerio_Lhx2                       CAGCGGKI--SDRYYL--LAVDK-QWHMRCL-KCCECKLNLESE-LTCFSKDGSIYCKEDYYRRFSVQR---CARCHLGISASEMVMRAR--DL-VYHLNCFTCTTCNKMLTTGDHFGMKD-SLVYC-RLHFETLIQ--SQKTKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRN
Danio_rerio_Lhx3                       CAGCNQHI--VDRFIL--KVLDR-HWHSKCL-KCSDCQSQLAD---KCFSRGDSVYCKDDFFKRFGT-K---CAACQQGIPPTQVVRRAQ--DF-VYHLHCFACIVCKRQLATGDEYYLMEDSRLVC-KADYETAKQ--DSTAKRPRTTITAKQLETLKNAYNNSPKPARHVREQLSTETGLDMRVVQVWFQNRRAKEKRL
Danio_rerio_Lhx4                       CAGCSQHI--LDKFIL--KVLDR-HWHSKCL-KCADCHALLAD---KCFSRAGNVYCKEDFFKRFGT-K---CASCQQGIPPTQVVRKAQ--DF-VYHLHCFACVMCSRQLATGDEFYLMEDGRLVC-KEDYETAKQ--ETGAKRPRTTITAKQLETLKSAYKNSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRL
Danio_rerio_Lhx5                       CAGCERPIL--DRFLL--NVLDR-AWHAKCV-QCCECNCNLTE---KCFSRDGKLYCKIDFFRRFGT-K---CAGCLQGISPSDLVRRAR--SK-VFHLNCFTCMVCNKQLSTGEELYVIDENKFVC-KEDYLSA-S--CTKRRGPRTTIKAKQLETLKAAFVATPKPTRHIREQLAQETGLNMRVIQVWFQNRRSKERRM
Danio_rerio_Lhx6                       CASCGLEI--LDRYLL--KVNNL-IWHVRCL-ECSVCRTSLRQH-SSCYIKNKEIFCKMDYFSRFGT-K---CARCGRQIYASDWVRRAR--GN-AYHLACFACFSCKRQLSTGEEFGLVE-EKVLC-RIHYDTMVE--PKPAKRARTSFTAEQLQVMQAQFAQDNNPDAQTLQKLADMTGLSRRVIQVWFQNCRARHKKH
Danio_rerio_Lhx8                       CTSCGTEI--VDKYLL--KVNDM-CWHVRCL-SCSVCQTSLGRH-ISCYIKEKEIFCKLDYFRKYGT-R---CAHCGRNIHSNDWVRRAK--GN-TYHLACFACFSCKRQLSTGEEFALVD-ERVLC-RVHYDCMLD--PKPAKRARTSFTADQLQVMQAQFAQDNNPDAQTLQKLAERTGLSRRVIQVWFQNCRARHKKH
Danio_rerio_Lmx1b2                     CEGCHRPI--SDRFLL--RMN-DSSWHEECL-QCSVCQQLLTMS---CYSRDHKLYCKHDYQQLFAT-K---CSGCLEKISPTELVMR-A-LES-VYHLSCFCCCVCERRLCKGDEFVLKE-GQLLC-KTDYEREK---RR-PKRPRTILTTQQRRAFKASFEVSSKPCRKVRETLAAETGLSVRVVQVWFQNQRAKMKKL
Drosophila_melanogaster_Apterus        CSGCGRQI--QDRFYL--SAVEK-RWHASCL-QCYACRQPLERE-SSCYSRDGNIYCKNDYYSFFGTRR---CSRCLASISSNELVMRAR--NL-VFHVNCFCCTVCHTPLTKGDQYGIID-ALIYC-RTHYSIARE--SSRTKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLSQKTGLPKRVLQVWFQNARAKWRRM
Drosophila_melanogaster_Arrowhead      CAACGEPI--SDRFFL--EVGGC-SWHAHCL-RCCMCMCPLDRQ-QSCFIRERQVYCKADYSKNFGA-K---CSKCCRGISASDWVRRAR--EL-VFHLACFACDQCGRQLSTGEQFALMD-DRVLC-KAHYLETVE--KSKTKRVRTTFTEEQLQVLQANFQIDSNPDDQDLERIASVTGLSKRVTQVWFQNSRARQKKH
'Drosophila melanogaster Lhx1/5'       CAGCNKPIL--DKFLL--NVLER-AWHASCV-RCCECLQPLTD---KCFSRESKLYCRNDFFRRYGT-K---CSGCGQGIAPSDLVRKPR--DK-VFHLNCFTCCICRKQLSTGEQLYVLDDNKFIC-KDDYLLGKA--GSKRRGPRTTIKAKQLEVLKTAFNQTPKPTRHIREQLAKETGLPMRVIQVWFQNKRSKERRM
'Drosophila melanogaster Lhx3/4'       CGGCHELI--LDRFIL--KVLER-TWHAKCL-QCSECHGQLND---KCFARNGQLFCKEDFFKRYGT-K---CSACDMGIPPTQVVRRAQ--DN-VYHLQCFLCAMCSRTLNTGDEFYLMEDRKLIC-KRDYEEAKA--DQPNKRPRTTITAKQLETLKTAYNNSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRL
Drosophila_melanogaster_Lmx1a          CAHCCQPI--CDRYIM--RVV-ENSFHEGCL-KCTACSLHLVHS---CYAREGKLYCRVDYERLYIRNH---CLGCGLKIAADELVMR-C-HEN-VFHLKCFACVVCGALLKKGEQYVVKQ-GQLFC-RFDYEKEVE--RRGPKRPRTILNTQQRRAFKASFEVSPKPCRKVRENLAKDTGLSLRIVQVWFQNQRAKVKKI
Drosophila_melanogaster_Lmx1b          CEGCGQKI--HDRFLM--NVG-DANWHEQCL-ACCYCGMQLHHT---CYVRNSKLYCKMDYDRLFGV-K---CSSCCHAILPQELVMRPI-PNF-VFHLPCFVCYACRLPLQKGEQFMLRD-GQLFCYRHDLEKEMF--RRGPKRPRTILTSQQRKQFKASFDQSPKPCRKVREALAKDTGLSVRVVQVWFQNQRAKMKKI
Drosophila_melanogaster_Tailup         CVGCGGQI--HDQYIL--RVAPDLEWHAACL-KCQECRQFLDES-CTCFVRDGKTYCKRDYVRLFGT-K---CDKCGNSFSKNDFVMRAK--TK-IFHIECFRCSACARQLLPGDEFALRDAGALYC-KEDHDVLEK--DGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTSLSPRVIRVWFQNKRCKDKKK
'Hydra magnipapillata Lhx1/5'          CSKCSLPMN--DKFVA--KILDM-IMHEDCI-RCFSCNCMLKD---TCYFRESKFFCKDHFFRFYGV-K---CVACKKRIDPLNMVHKYK--EN-LIHVACLRCCFCNREATTGEEIHITENFTFVC-KEDFEKYQN--INKSRGPRTVINLKQLEVLKETFKVNQKPSRLEREKLATKTGLTTRVIQVWFQNKRSKERRF
'Hydra magnipapillata Lhx6/8a'         CDACHEIIY--DRYIS--I?GNR-KLHEECL-QCSSCSVSVSLSG-RCYEKNEQIFCEECYHLNFSL-V--QCKGCSQSIMKSEYVMKTQ--EN-FYHVYCFRCNLCNSMLQSGERYGVKG-DKLFC-EAHYYGNNA--LMKEKRYRTTFTQEQVELMQKAFEIERNPDSASLQQLSKEINLSKRVLQVWFQNARAKHKKL
'Hydra magnipapillata Lhx6/8b'         -------------------------------------------------MHSTEISCEGNAN-LLKI-K---CSSCSRPIQLTDWIRRAK--QN-VYHLACFSCDICKRQLSTGEEFAFIE-DSILC-KLHYVEHLE--ENKNKRVRTSFTDEQVLILQANFDLDANPDSNELERIAADVSLPKRVTQVWFQNSRARQKKQ
Hydra_magnipapillata_Lmx1              CHECKSPIL--DSFLL--NIGGNEYWHECCL-KCHECCEKLFR---VCYKKDGGVYCKYDYKRLFGI-K---CVACNNIITPNSIAMKVL--DTNLFHIDCFKCQNCGKMLEKGEEYAFKN-QKLLC-KADFNTEHI-----YKRPRTILTTQQRQNFKTAFEQAPKPCRKIREKLSKETGLSVRVVQVWFQNQRAKLKKL
Lottia_gigantea_Islet1                 CVGCGSNI--HDQFIL--RVAPDLEWHASCL-KCADCNQYLDET-CTCFVRDGKTYCKRDYVRLFGT-K---CSKCSQGFSKSDFVMRAR--GQ-VFHIDCFRCVACSRQLIPGDEFALRE-DGIFC-KDDHDVVEK--DHKTTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQMTEMTGLSPRVIRVWFQNKRCKDKKR
'Lottia gigantea Lhx1/5'               CAGCERPIS--DRFLL--NVLDR-AWHAKCV-QCFDCKNNLTE---KCFYREGKLYCRLDFFRRYGT-K---CAGCSHGISPNDLVRRAR--NK-VFHLKCFTCMVCRKQLSTGEELYILDENKFIC-KEDYINSKF--GAKRRGPRTTIKAKQLEVLKAAFNATPKPTRHIREQLAQETGLNMRVIQVWFQNRRSKERRM
'Lottia gigantea Lhx2/9'               ------------------MAVDK-QWHVQCL-KCSDCKLPLDSE-LTCFARDGCIYCKDDYYRRFGVKR---CARCHLGIAANELVMRAR--DV-VYHLSCFTCNACNRPLTTGEQFGMKD-HLVYC-RTDYEMMFQ--GSRQKRVRTSFKHHQLRTMKSYFALNHNPDAKDLKQLAQKTGLNKRVLQVWFQNARAKYRRN
'Lottia gigantea Lhx3/4'               -------------FIL--KVLER-SWHSKCL-KCADCQIQLSD---KCFSKGDHVYCKEDFFQRFGT-K---CAACEKGIPPTEIVRRAQ--DY-VYHLDCFACLMCSEKLKTGDEFYLMEDKKLVC-KEDYETAKA--DSSNKRPRTTINAKQLENLKRAYNESAKPARHVREQLSAETGLDMRVVQVWFQNRRAKEKRL
'Lottia gigantea Lhx6/8'               CFGCGGMI--HDRYLL--RVNGC-SFHVDCL-RCSVCDCVLERQ-SSCFIKGDNIYCKVDYTREYGA-K---CSKCQRHIQPNDWVRRAR--DN-VYHLACFACDSCKRQLSTGEEFALQD-DRVLC-KTHYIEVLE--KQKAKRVRTTFSEEQVQVLQANFNIDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKY
Lottia_gigantea_Lmx1                   CTGCQMSI--EDKFLL--KVM-DNSWHETCL-NCAMCQLPLSGS---CFVRDRKLYCRADYDKLFGT-K---CNGCLQSIPANELVMR-A-AGY-VYHLRCFMCMACGHQLQKGDEFVVKE-GQLFC-RLDFEKEFS--K-GPKRPRTILNTSQRRKFKAAFELNPKPCRKVREALAAETGLSVRVVQVWFQNQRAKVKKI
Mnemiopsis_leidyi_Islet                CAGCRCPI--TDQFIL--RVAPNLEWHASCL-KCDDCNKFLDEN-CTCFIREGKPYCKKDFVR-FGA-K---CHRCDQGFSSNDFVMRVR--EN-IFHLSCFRCNMCSRQLVPGEEFALLP-EGLIC-GTHIKQQHH--EQKTTRVRTVLNDRQLRILRTCYNNNPRPDALMKEQMTKLTGLSARVIRVWFQNKRCKDKKK
'Mnemiopsis leidyi Lhx1/5'             CAGCNGKIH--DKFLM--KVLDK-TWHSECL-VCVDCGVVLAD---QCFTRNGKFYCSKDFEKSQAS-S---CGACKKDITPDDMILKPPNTVG-MFHVKCFTCSKCSRQLEAGEEFYTIDNKKFLC-SRDFKNHRS--TGKRRGPRTTIKSKQLDILKAAFKSNQKPTRNIREQLATETGLNMRVIQVWFQNRRSKERRM
'Mnemiopsis leidyi Lhx3/4'             CAGCDQPI--TDRFIL--KVMEK-NWHSACL-KCHDCLAQLTD---KCFSRGDFVYCKDDFYKRYGT-K---CAKCEKVIPPSQVVRRAG--GH-VFHMDCFVCIICSRTLNTGDEFYFVDDNQLVC-RSDYDNFKT--NQGIKRPRTTITAKQLETLKTAYENSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRM
Mnemiopsis_leidyi_Lmx1                 CTACRLPIE--ESLLM--KVNDV-FWHEQCL-RCCLCNVPLSDS--CFFDKHQRLYCKADHYQRILD-AS-TCCTCNGSINANDLVYRVH--GS-LYHIRCFTCTRCSSSLRKGDEYVMHGNGDLVC-KTCSDDGLR--KRPRTVLSSVQRKEHLSVFKEAFDRTPRPCRKEREKLSSQTGLSVRVVQVWFQNQRAKVKKL
Mus_musculus_Islet1                    CVGCGNQI--HDQYIL--RVSPDLEWHAACL-KCAECNQYLDES-CTCFVRDGKTYCKRDYIRLYGI-K---CAKCSIGFSKNDFVMRAR--SK-VYHIECFRCVACSRQLIPGDEFALRE-DGLFC-RADHDVVER--PEKTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR
Mus_musculus_Lhx1                      CAGCKRPIL--DRFLL--NVLDR-AWHVKCV-QCCECKCNLTE---KCFSREGKLYCKNDFFRCFGT-K---CAGCAQGISPSDLVRRAR--SK-VFHLNCFTCMMCNKQLSTGEELYIIDENKFVC-KEDYLSNSS--GAKRRGPRTTIKAKQLETLKAAFAATPKPTRHIREQLAQETGLNMRVIQVWFQNRRSKERRM
Mus_musculus_Lhx2                      CAGCGGKI--SDRYYL--LAVDK-QWHMRCL-KCCECKLNLESE-LTCFSKDGSIYCKEDYYRRFSVQR---CARCHLGISASEMVMRAR--DL-VYHLNCFTCTTCNKMLTTGDHFGMKD-SLVYC-RLHFEALLQ--SQKTKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRN
Mus_musculus_Lhx3                      CAGCDQHI--LDRFIL--KALDR-HWHSKCL-KCSDCHVPLAE---RCFSRGESVYCKDDFFKRFGT-K---CAACQLGIPPTQVVRRAQ--DF-VYHLHCFACVVCKRQLATGDEFYLMEDSRLVC-KADYETAKQ--EATAKRPRTTITAKQLETLKSAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRL
Mus_musculus_Lhx4                      CAGCNQHI--LDKFIL--KVLDR-HWHSSCL-KCADCQMQLAD---RCFSRAGSVYCKEDFFKRFGT-K---CTACQQGIPPTQVVRKAQ--DF-VYHLHCFACIICNRQLATGDEFYLMEDGRLVC-KEDYETAKQ--EAGAKRPRTTITAKQLETLKNAYKNSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRL
Mus_musculus_Lhx5                      CAGCERPIL--DRFLL--NVLDR-AWHIKCV-QCCECKTNLSE---KCFSREGKLYCKNDFFRRFGT-K---CAGCAQGISPSDLVRKAR--SK-VFHLNCFTCMVCNKQLSTGEELYVIDENKFVC-KDDYLSS-S--GTKRRGPRTTIKAKQLETLKAAFAATPKPTRHIREQLAQETGLNMRVIQVWFQNRRSKERRM
Mus_musculus_Lhx6                      CSSCGLEI--LDRYLL--KVNNL-IWHVRCL-ECSVCRTSLRQQ-NSCYIKNKEIYCKMDYFSRFGT-K---CARCGRQIYASDWVRRAR--GN-AYHLACFACFSCKRQLSTGEEFGLVE-EKVLC-RIHYDTMIE--PKPAKRARTSFTAEQLQVMQAQFAQDNNPDAQTLQKLADMTGLSRRVIQVWFQNCRARHKKH
Mus_musculus_Lhx8                      CSSCGLEI--VDKYLL--KVNDL-CWHVRCL-SCSVCRTSLGRH-TSCYIKDKDIFCKLDYFRRYGT-R---CSRCGRHIHSTDWVRRAK--GN-VYHLACFACFSCKRQLSTGEEFALVE-EKVLC-RVHFDCMLD--PKPAKRARTSFTADQLQVMQAQFAQDNNPDAQTLQKLAERTGLSRRVIQVWFQNCRARHKKH
Mus_musculus_Lhx9                      CAGCGGKI--SDRYYL--LAVDK-QWHLRCL-KCCECKLALESE-LTCFAKDGSIYCKEDYYRRFSVQR---CARCHLGISASEMVMRAR--DS-VYHLSCFTCFTCNKTLTTGDHFGMKD-SLVYC-RAHFETLLQ--SQKTKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRN
Mus_musculus_Lmo4                      CAGCGGKIA--DRFLL--YAMDS-YWHSRCL-KCSCCQAQLGDIGTSCYTKSGMILCRNDYIRLFGN-SG-ACSACGQSIPASELVMRAQ--GN-VYHLKCFTCSTCRNRLVPGDRFHYIN-GSLFC-EHDRPTALI---------SNPLLPDQKVC--------------------------------------------
Mus_musculus_Lmx1a                     CEGCQRVI--SDRFLL--RLN-DSFWHEQCV-QCASCKEPLETT---CFYRDKKLYCKYHYEKLFAV-K---CGGCFEAIAPNEFVMR-A-QKS-VYHLSCFCCCVCERQLQKGDEFVLKE-GQLLC-KGDYEKERE--KR-PKRPRTILTTQQRRAFKASFEVSSKPCRKVRETLAAETGLSVRVVQVWFQNQRAKAQTN
Nematostella_vectensis_Islet           CVGCGSQI--HDQYIL--RVAPDLEWHASCL-KCADCHMYLDEK-CTCFVREGKTYCKRDYVRLFGT-K---CAKCSLNFSKNDFVMRAR--NK-IYHIDCFRCVACSRQLVPGDEFALRE-DGLFC-KADHEIVEK--TDRPTRVRTVLNEKQLHTLRTCYNANPRPDAMMKEQLVEMTGLSPRVIRVWFQNKRCKDKKK
'Nematostella vectensis Lhx1/5'        CAGCQLPIA--DKFLL--KVLDG-VWHAQCV-QCSDCKCPLTE---RCFSREGKLFCKTDFYRRYGT-K---CSGCDQGISPNDMVRRAK--HL-VFHVDCFVCSYCKRQITTGDELYYIGDGSFIC-RDDYYHS-H--ASKRRGPRTTIKAKQLEALKSTFAATPKPSRNIREKLAQETGLNMRVIQVWFQNRRSKERRL
'Nematostella vectensis Lhx2/9'        CAGCGSRI--LERFYL--MAVDQ-EWHADCL-KCSDCELRLDNE-LTCFSKDGVILCREDYYRRFSVKK---CSSCSQAISSKELVMRAR--DQ-VYHVNCFACDRCKRMLATGEYFGMRG-IRIYC-KEDYEELLR--DGRPKRVRTSFKHHQLRAMKTYFAMNHNPDAKDLKQLSQKTGLTKRVLQVWFQNARAKFRRT
'Nematostella vectensis Lhx3/4-like'   CAGCDEQFGHADRFIL--QALDR-HWS?-CI-RCTDCDESLDV---KCYVREGRVFCPSDYFRRFGP-K---CASCNKDIQPSQMVHKVD--SN-VYHITCLSCVTCQQQLETRDEFFLLEDGKVIC-RNDYGDRDE--SSRSKRARTFISNDQLAFLKVAYASSPKTTLRDRERIAKETGLDMRVVQVWFQNRRAKDKRL
'Nematostella vectensis Lhx6/8'        CVGCEAKI--VDRYLV--KVSGR-AWHTKCL-KCCLCSDELGRE-ATCYTKDGKIYCKADYARQFGT-K---CARCGRSIHANDWVRRAK--NC-VYHLACFACDNCKRQLSTGEEFALKD-GHVLC-KLHYLEALD--RHKAKRVRTTFTEDQLQILQANFNIDSNPDGQDLERIAQLTGLSKRVTQVWFQNSRARQKKY
Nematostella_vectensis_Lmo4            CAGCGEKII--DRFLL--LALDQ-YWHVNCL-KCSCCEARLGEIGTSCYSKGGMILCKTDYVRLYGN-SG-ACAVCAKLIPATELVMKVL--GK-VYHLHCFTCTTCHNQLVPGDRFHVVN-GRLFC-ENDDP-NLL--------------TKQTVC--------------------------------------------
Nematostella_vectensis_Lmx1            CTGCNEPI--EDRFLM--KVV-DEAWHESCL-QCCICRSQLSRS---CFSKDRKLYCRTDYEKTFGH-R-----------------------TT-IWHLSFAVCTDN--VFEKSLCLS------LPCC-----------KKGPKRPRTILTSQQRKVFKSAFEISSKPCRKVREELSRETGLSVRVVQVWFQNQRAKVQK-
Saccoglossus_kowalevskii_Islet1        CVGCGNQI--QDQFIL--RVAPDLEWHASCL-KCTDCNQYLDET-CTCFVRDSKTYCKRCYVRLFGT-K---CAKCNLGFSKNDFVMRAR--NK-IFHIDCFRCVACSRQLIPGDEFALRD-DGLFC-KADHDVVER--HHKTTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLTEMTNLSPRVIRVWFQNKRCKDKKR
'Saccoglossus kowalevskii Lhx1/5'      CAGCDRPIL--DRFLL--NVLDR-AWHVKCV-QCSDCNCTLSD---KCYSREGKLYCRTDFVRRYGT-K---CAGCSHGIAPNDLVRRAR--NK-VFHLKCFTCMVCSKQLSTGEELYVVDENQYIC-KDDYLGSKS--GTKRRGPRTTIKAKQLETLKAAFAATPKPTRHIREQLAQETGLNMRVIQVWFQNRRSKERRM
'Saccoglossus kowalevskii Lhx2/9'      CAGCGGRI--LDRYYL--LAVDK-QWHMQCL-KCCECKLRLDSE-LTCFAKDGSIYCKDDYYRRFSVKR---CARCHLGISASEMVMRAR--DL-VYHLSCFTCATCNKALATGDHFGMKD-AMVYC-RSHYEAMLH--QQRTKRMRTSFKHHQLRTMKSYFALNHNPDAKDLKQLAQKTGLTKRVLHVWFQNARAKYRRS
'Saccoglossus kowalevskii Lhx3/4'      CSGCEHPI--LDRFIL--KVQDR-AWHSKCL-KCTDCQAQLSD---KCYSRGGQVYCKEDFFKRFGT-K---CSACDQGIPPTQVVRRAQ--DN-VYHLQCFACVMCNRQLATGDEFYLMNDNKLVC-KGDYEAAKV--DASNKRPRTTISAKQLETLKTAYANSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRL
'Saccoglossus kowalevskii Lhx6/8'      CLGCTSPI--QDRYLL--KVGTR-SWHVRCL-RCCICQTGLGGQ-QSCFTKDDNIYCKMDYIRQFGT-K---CSRCMRNIQSNDWVRKAK--NH-VYHLACFACDNCKRQLSTGEEFAMQE-NKVLC-KTHYLELLE--NPRTKRVRTTFTEEQLQVLQANFNVDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH
Saccoglossus_kowalevskii_Lmo4          CAGCGVKIM--DRFLL--HALDR-YWHTGCL-KCTCCGAQLGELGPSCFSKGGMILCKKDYLRLFGN-SG-ACSSCGQSIPASELVMRAQ--GN-VYHQKCFACTSCHNQLVPGDRFLIVN-GNLFC-ETDHL-KIL------------IRARNKVC--------------------------------------------
Saccoglossus_kowalevskii_Lmx1          CAGCQQPI--EDRFLM--RVM-ENSWHEQCL-QCSVCQSPLSRS---CYFKDRKLYCKGDYEKLFGT-K---CNGCLQSITSNELVMR-A-LCN-VYHLRCFNCIICNQRLQKGDEFVVRD-NQLFC-KVDYEKEYG--RKGPKRPRTILTTAQRRAFKQSFEVSQKPCRKVRESLAADTGLSVRVVQVWFQNQRAKMKKI
Tribolium_castaneum_Arrowhead          CSACGEPI--SDKFLL--EVSGR-SWHARCL-RCCVCQLQLDRQ-PSCFIRDRAIYCKADYAKSFGA-K---CSVCSRGISSSDWVRKAR--DH-VYHLACFACAACHRQLSTGEEFALHE-DRVLC-KAHYLETLD--KNKAKRVRTTFTEEQLQVLQANFQLDSNPDGQDLERIAQITGLSKRVTQVWFQNSRARQKKH
'Tribolium castaneum Lhx1/5'           CAACDKPIL--DKFLL--NVLER-TWHADCV-RCFDCHAPLTD---KCFSRENKLFCRNDFFRRYGT-K---CGGCGQGISPSDLVRKAR--DK-VFHLNCFTCLVCRKQLSTGEELYVLDDNKFIC-KDDYLNGNK--GSKRRGPRTTIKAKQLEILKTAFSQTPKPTRHIREQLAKETGLPMRVIQVWFQNKRSKERRL
'Tribolium castaneum Lhx3/4'           CGGCHELI--LDRFIL--KVADR-TWHAKCL-QCSDCRIQLTD---KCFARNGQLFCKEDFFKRFGT-K---CAGCDLGIPPTQVVRRAQ--DN-VYHLQCFSCVMCARQLNTGDEFYLMEDRKLVC-KPDYEAAKS--DQPNKRPRTTITAKQLETLKNAYNNSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRL
Tribolium_castaneum_Lmx1a              --MCCRPI--NDRFLL--RIM-DVSYHEHCV-QCCACGDRLHHT---CFVKDSKLYCRLDYDRLFVK-K---CLACSERIAPEELVMR-A-SEN-IFHLRCFVCVVCGIRLQKGDLYVIKQ-GQLFC-RIDYEKEVE--RRGPKRPRTILTTQQRRAFKASFEVSPKPCRKVREALAKDTGLSVRIVQVWFQNQRAKMKKM
Tribolium_castaneum_Lmx1b              CEGCGQKI--HDRYLM--RVA-DASWHEHCL-TCSICGVQLAHS---CYTRNTKLYCKADYDRIFGV-K---CSRCGDRLLPHEMVMR-A-QQH-VFHLPCFVCVVCCQPLQKGEQFVLRA-GQLFC-RQDFEKEMY--RRGPKRPRTILTSAQRRQFKASFEVSPKPCRKVREALAKETGLSVRVVQVWFQNQRAKMKKI
Trichoplax_adhaerens_Islet             CSGCGGKI--NDRYIL--QVAPDMQYHAACL-KCASCQQLLDEK-ETCFLRNGKPYCKSDFKMLFHN-R---CTKCNRIFEPSEFIMRAK--GN-PYHIDCFRCHSCMRKLIPGDRYGVDT-YILYC-KEHY--LNK--GMKGTRIRTVLNEKQLQTLRSYYASNPRPDSTVKEKLVELTGLNPRVIRVWFQNKRCKDKKI
'Trichoplax adhaerens Lhx1/5a'         CTGCNQLI--QDKFLL--KVADD-LWHEDCL-RCYKCTQPLSK---SCYIKDHKLYCKEDYDKRFGR-K---CQGCNLGILPDEMVYRLH--GS-CYHINCLLCIVCSRQFKVGDKYYISDEGKPIC-KEDYDVAIM--HPNLKRPRTSITQQQLKMLNSVYRIKPRPSRITREMIATKVGLDLRVVQVWFQNKRAKDKRS
'Trichoplax adhaerens Lhx1/5b'         CAGCQLPIC--DKFLL--SVLDR-KWHTKCV-QCSQCKVQLSE---KCFSRDGKLYCRNDFYRTYGT-K---CSGCGIGIPPNELVRRAR--DD-VYHIKCLKCAICGRQMSTGEQLYINQHNQYIC-QADYQNSIS--NCKKRGPRTTIKTEQLEMLKNAFAITPKPTRLIRERLAQQTGLNMRVIQVWFQNRRSKERRV
'Trichoplax adhaerens Lhx2/9'          CAGCGRSI--MDQEYLGIQKTDK-KWHIQCL-RCYDCNEPLDKD-QSCYVKQGNIFCRTDYFNRFGSIK---CPTCNSGISPKEHVMKAR--EY-AYHCSCFICHTCNRLLKTGEEFAMRG-CKLYC-KEHFQSITS--HGRSKRIRTSFKQPQLRTMKTYFALNHNPDSKDLKQLSIKTGLNKRVLQVWFQNARAKYRRS
;
END;

[ The following blocks are output data for analysis step 14283 ]
BEGIN TREES;
      TITLE 'Results of the LhX/Lim transcription factor gene family';
      LINK TAXA = TaxaForAnalysisStep14283;
      TREE IQPNNI_ML_consensus_tree = [&R] (Danio_rerio_Lmx1b2:0.07067,(((Tribolium_castaneum_Lmx1a:0.15831,Drosophila_melanogaster_Lmx1a:0.26641)98:0.12441,(Tribolium_castaneum_Lmx1b:0.08006,Drosophila_melanogaster_Lmx1b:0.21761)94:0.19573)81:0.16382,((Nematostella_vectensis_Lmx1:0.3313,Acropora_digitifera_Lmx1:0.06451)99:0.20291,((((Nematostella_vectensis_Lmo4:0.22694,Mus_musculus_Lmo4:0.2012)50:1.0E-5,Saccoglossus_kowalevskii_Lmo4:0.19386)100:0.58398,((((Danio_rerio_Islet:0.00513,Mus_musculus_Islet1:0.00562)99:0.086,(Lottia_gigantea_Islet1:0.03493,Mnemiopsis_leidyi_Islet:0.42983)59:0.04983,(Nematostella_vectensis_Islet:0.03686,Acropora_digitifera_Islet:0.10297)50:0.05559,Branchiostoma_floridae_Islet1:0.0724,Saccoglossus_kowalevskii_Islet1:0.0725,Ciona_intestinalis_Islet1:0.13623,Drosophila_melanogaster_Tailup:0.19136)56:0.16565,Trichoplax_adhaerens_Islet:0.58135)100:0.54379,((((Danio_rerio_Lhx6:0.00675,Mus_musculus_Lhx6:0.01999)97:0.1184,(Mus_musculus_Lhx8:0.02471,Danio_rerio_Lhx8:0.06898)75:0.05243)100:0.35874,(('Nematostella vectensis Lhx6/8':0.05352,'Acropora digitifera Lhx6/8':0.11343)99:0.19706,((('Hydra magnipapillata Lhx6/8b':0.1541,'Cladonema pacificum Lhx6/8':0.08682)99:0.48656,(Tribolium_castaneum_Arrowhead:0.09083,Drosophila_melanogaster_Arrowhead:0.16046)77:0.15482,'Lottia gigantea Lhx6/8':0.17782)55:0.06933,'Saccoglossus kowalevskii Lhx6/8':0.13052)46:0.05133,'Branchiostoma floridae Lhx6/8':0.14372)82:0.153)82:0.26397,(((((((Danio_rerio_Lhx2:0.00528,Mus_musculus_Lhx2:0.00527)83:0.0241,Mus_musculus_Lhx9:0.02552)64:0.03797,'Branchiostoma floridae Lhx2/9':0.26663)66:0.0484,'Saccoglossus kowalevskii Lhx2/9':0.04829)77:0.10842,'Lottia gigantea Lhx2/9':0.08384,Drosophila_melanogaster_Apterus:0.44606)53:0.15703,'Nematostella vectensis Lhx2/9':0.27897,'Trichoplax adhaerens Lhx2/9':0.51578)88:0.30717,'Hydra magnipapillata Lhx6/8a':1.267)49:0.15512)93:0.22917)57:0.14704)55:0.06165,(((('Tribolium castaneum Lhx1/5':0.05839,'Drosophila melanogaster Lhx1/5':0.08839)94:0.19464,(((Danio_rerio_Lhx1:0.01629,Mus_musculus_Lhx1:0.02422)73:0.0225,Mus_musculus_Lhx5:0.01716)60:0.00729,Danio_rerio_Lhx5:0.04523)90:0.07586,((('Acropora millepora Lhx1/5':1.0E-5,'Acropora digitifera Lhx1/5':0.00556)99:0.11313,'Nematostella vectensis Lhx1/5':0.12034)83:0.01244,'Hydra magnipapillata Lhx1/5':1.02761)50:0.21907,'Mnemiopsis leidyi Lhx1/5':0.76732,'Ciona intestinalis Lhx1/5':0.89432,'Saccoglossus kowalevskii Lhx1/5':0.0904,'Lottia gigantea Lhx1/5':0.10317,'Branchiostoma floridae Lhx1/5':0.15739,'Trichoplax adhaerens Lhx1/5b':0.41781)56:0.14895,'Amphimedon queenslandica Lhx1/5':0.65528)94:0.25208,(('Tribolium castaneum Lhx3/4':0.03894,'Drosophila melanogaster Lhx3/4':0.08186)99:0.14936,((Mus_musculus_Lhx4:0.03543,Danio_rerio_Lhx4:0.04424)94:0.05144,(Danio_rerio_Lhx3:0.03282,Mus_musculus_Lhx3:0.06889)73:0.02473)84:0.09914,('Ciona intestinalis Lhx3/4':0.17808,'Mnemiopsis leidyi Lhx3/4':0.2636)67:0.08288,'Branchiostoma floridae Lhx3/4':0.13286,'Lottia gigantea Lhx3/4':0.19133,'Saccoglossus kowalevskii Lhx3/4':0.10887,'Amphimedon queenslandica Lhx3/4':0.27924)80:0.20733,'Nematostella vectensis Lhx3/4-like':0.78902,'Trichoplax adhaerens Lhx1/5a':0.90232)54:0.15457)93:0.46351,Hydra_magnipapillata_Lmx1:0.84603,Mnemiopsis_leidyi_Lmx1:1.1679)49:0.17569,Lottia_gigantea_Lmx1:0.26275,Saccoglossus_kowalevskii_Lmx1:0.14622)99:0.21987,Mus_musculus_Lmx1a:0.21316);
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr76765]


END;
BEGIN TREES;
      TITLE 'Results of the LhX/Lim transcription factor gene family';
      LINK TAXA = TaxaForAnalysisStep14283;
      TREE BioNJ_consensus_tree = [&R] (Danio_rerio_Lmx1b2:0.0636,((Nematostella_vectensis_Lmx1:0.34625,Acropora_digitifera_Lmx1:0.06158)93:0.32174,(((((Nematostella_vectensis_Lmo4:0.23583,Mus_musculus_Lmo4:0.21979)52:1.0E-5,Saccoglossus_kowalevskii_Lmo4:0.1887)100:0.60526,(((((Danio_rerio_Islet:0.00525,Mus_musculus_Islet1:0.0058)99:0.09053,(Branchiostoma_floridae_Islet1:0.06056,Saccoglossus_kowalevskii_Islet1:0.07121)48:0.01367,Nematostella_vectensis_Islet:0.0823,Acropora_digitifera_Islet:0.14,Lottia_gigantea_Islet1:0.09619,Ciona_intestinalis_Islet1:0.13749,Drosophila_melanogaster_Tailup:0.19864)80:0.1171,Trichoplax_adhaerens_Islet:0.67357)64:0.00257,Mnemiopsis_leidyi_Islet:0.36939)100:0.61587,((((Danio_rerio_Lhx6:0.00691,Mus_musculus_Lhx6:0.02054)100:0.12138,(Mus_musculus_Lhx8:0.02457,Danio_rerio_Lhx8:0.0718)98:0.05464)100:0.35697,(('Nematostella vectensis Lhx6/8':0.05556,'Acropora digitifera Lhx6/8':0.11548)100:0.21664,(Tribolium_castaneum_Arrowhead:0.07804,Drosophila_melanogaster_Arrowhead:0.18036)84:0.229,((('Hydra magnipapillata Lhx6/8b':0.19697,'Cladonema pacificum Lhx6/8':0.05781)100:0.46974,'Lottia gigantea Lhx6/8':0.11356)56:0.11738,'Saccoglossus kowalevskii Lhx6/8':0.13634)53:0.043,'Branchiostoma floridae Lhx6/8':0.17261)64:0.1695)73:0.27993,(((((((Danio_rerio_Lhx2:0.00547,Mus_musculus_Lhx2:0.00536)89:0.02498,Mus_musculus_Lhx9:0.02403)93:0.07046,'Saccoglossus kowalevskii Lhx2/9':0.06899)92:0.06518,'Lottia gigantea Lhx2/9':0.13893)62:0.03114,'Branchiostoma floridae Lhx2/9':0.28544)53:0.12562,'Nematostella vectensis Lhx2/9':0.33322,Drosophila_melanogaster_Apterus:0.41734,'Trichoplax adhaerens Lhx2/9':0.58267)92:0.33853,'Hydra magnipapillata Lhx6/8a':1.28115)49:0.15973)86:0.18008)61:0.22155)65:0.05777,((((('Acropora millepora Lhx1/5':1.0E-5,'Acropora digitifera Lhx1/5':0.00571)100:0.12118,'Nematostella vectensis Lhx1/5':0.12307)92:0.18059,(('Tribolium castaneum Lhx1/5':0.061,'Drosophila melanogaster Lhx1/5':0.09129)99:0.17611,((((Danio_rerio_Lhx1:0.01677,Mus_musculus_Lhx1:0.02508)82:0.02324,Mus_musculus_Lhx5:0.01777)63:0.00833,Danio_rerio_Lhx5:0.04612)93:0.06785,'Saccoglossus kowalevskii Lhx1/5':0.0902,'Lottia gigantea Lhx1/5':0.09518,'Branchiostoma floridae Lhx1/5':0.16553)60:0.03422)75:0.05843,(('Mnemiopsis leidyi Lhx1/5':0.46293,'Hydra magnipapillata Lhx1/5':0.90749)52:0.16797,'Ciona intestinalis Lhx1/5':0.78844)47:0.07689,'Trichoplax adhaerens Lhx1/5b':0.37868)63:0.13685,'Amphimedon queenslandica Lhx1/5':0.65629)77:0.21076,((('Tribolium castaneum Lhx3/4':0.03991,'Drosophila melanogaster Lhx3/4':0.08455)100:0.15497,((Mus_musculus_Lhx4:0.03628,Danio_rerio_Lhx4:0.04576)90:0.05364,(Danio_rerio_Lhx3:0.03338,Mus_musculus_Lhx3:0.07116)78:0.02496)92:0.10223,('Ciona intestinalis Lhx3/4':0.18416,'Mnemiopsis leidyi Lhx3/4':0.271)58:0.08727,'Branchiostoma floridae Lhx3/4':0.13596,'Lottia gigantea Lhx3/4':0.19751,'Saccoglossus kowalevskii Lhx3/4':0.11107,'Amphimedon queenslandica Lhx3/4':0.28985)86:0.15251,'Nematostella vectensis Lhx3/4-like':0.79579)44:0.06649)49:0.13101)62:0.14833,'Trichoplax adhaerens Lhx1/5a':0.75143)92:0.42503,(((Tribolium_castaneum_Lmx1b:0.08904,Drosophila_melanogaster_Lmx1b:0.21393)96:0.20496,(Tribolium_castaneum_Lmx1a:0.15588,Drosophila_melanogaster_Lmx1a:0.28234)96:0.12413)97:0.1791,Lottia_gigantea_Lmx1:0.25045,Saccoglossus_kowalevskii_Lmx1:0.14733)47:0.06482,Hydra_magnipapillata_Lmx1:0.98752,Mnemiopsis_leidyi_Lmx1:1.21791)97:0.22519,Mus_musculus_Lmx1a:0.22649);
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr76766]


END;
BEGIN TREES;
      TITLE 'Results of the LhX/Lim transcription factor gene family';
      LINK TAXA = TaxaForAnalysisStep14283;
      TREE PhyML_ML_tree = [&R] ('Hydra magnipapillata Lhx6/8b':0.185161,'Cladonema pacificum Lhx6/8':0.072937,('Lottia gigantea Lhx6/8':0.112367,((Tribolium_castaneum_Arrowhead:0.101565,Drosophila_melanogaster_Arrowhead:0.149157)51:0.147474,('Saccoglossus kowalevskii Lhx6/8':0.132936,('Branchiostoma floridae Lhx6/8':0.150048,(('Nematostella vectensis Lhx6/8':0.054846,'Acropora digitifera Lhx6/8':0.118364)96:0.150101,(((Danio_rerio_Lhx6:0.007128,Mus_musculus_Lhx6:0.018823)89:0.11777,(Mus_musculus_Lhx8:0.021607,Danio_rerio_Lhx8:0.069074)46:0.052206)99:0.39663,('Hydra magnipapillata Lhx6/8a':1.690309,((('Lottia gigantea Lhx2/9':0.078355,(Drosophila_melanogaster_Apterus:0.46665,('Saccoglossus kowalevskii Lhx2/9':0.048122,('Branchiostoma floridae Lhx2/9':0.26875,(Mus_musculus_Lhx9:0.026063,(Danio_rerio_Lhx2:0.005077,Mus_musculus_Lhx2:0.005184)79:0.022785)63:0.040209)57:0.044626)62:0.081396)13:0.028906)30:0.099668,('Trichoplax adhaerens Lhx2/9':0.542125,'Nematostella vectensis Lhx2/9':0.273539)31:0.093975)87:0.425951,(((Trichoplax_adhaerens_Islet:0.632678,(Drosophila_melanogaster_Tailup:0.080945,(Branchiostoma_floridae_Islet1:0.044161,((Acropora_digitifera_Islet:0.108578,Nematostella_vectensis_Islet:0.033461)33:0.045428,((Danio_rerio_Islet:0.004832,Mus_musculus_Islet1:0.005882)98:0.082793,(Ciona_intestinalis_Islet1:0.128749,(Saccoglossus_kowalevskii_Islet1:0.049112,(Lottia_gigantea_Islet1:0.040078,Mnemiopsis_leidyi_Islet:0.446876)49:0.022241)34:0.014168)11:0.007611)6:0.013986)1:0.01282)8:0.091931)23:0.107618)100:0.622156,(Nematostella_vectensis_Lmo4:0.230567,(Mus_musculus_Lmo4:0.193064,Saccoglossus_kowalevskii_Lmo4:0.191048)32:2.0E-6)100:0.640803)33:0.098265,((Mnemiopsis_leidyi_Lmx1:1.163837,((Lottia_gigantea_Lmx1:0.234495,(Saccoglossus_kowalevskii_Lmx1:0.134845,((Danio_rerio_Lmx1b2:0.073383,Mus_musculus_Lmx1a:0.22807)99:0.186023,((Tribolium_castaneum_Lmx1a:0.14927,Drosophila_melanogaster_Lmx1a:0.304762)98:0.129468,(Tribolium_castaneum_Lmx1b:0.086713,Drosophila_melanogaster_Lmx1b:0.217481)88:0.202214)76:0.153206)25:0.073244)27:0.065012)45:0.12425,(Hydra_magnipapillata_Lmx1:1.008598,(Nematostella_vectensis_Lmx1:0.354829,Acropora_digitifera_Lmx1:0.083097)98:0.142784)15:0.062539)52:0.087915)79:0.424489,('Trichoplax adhaerens Lhx1/5a':0.976858,(('Amphimedon queenslandica Lhx1/5':0.769247,(('Branchiostoma floridae Lhx1/5':0.14081,(('Lottia gigantea Lhx1/5':0.093464,'Saccoglossus kowalevskii Lhx1/5':0.083594)24:0.007462,(('Tribolium castaneum Lhx1/5':0.067352,'Drosophila melanogaster Lhx1/5':0.081199)92:0.187835,(Danio_rerio_Lhx5:0.045069,(Mus_musculus_Lhx5:0.017268,(Danio_rerio_Lhx1:0.016645,Mus_musculus_Lhx1:0.023422)71:0.023351)49:0.007022)78:0.043125)16:0.021904)22:0.026757)29:0.032088,(('Mnemiopsis leidyi Lhx1/5':0.654797,'Ciona intestinalis Lhx1/5':0.837755)32:0.108797,('Trichoplax adhaerens Lhx1/5b':0.385284,('Hydra magnipapillata Lhx1/5':1.139227,('Nematostella vectensis Lhx1/5':0.126806,('Acropora millepora Lhx1/5':0.0,'Acropora digitifera Lhx1/5':0.00548)97:0.117784)89:0.052133)31:0.129883)9:0.003528)12:0.030801)50:0.095869)92:0.233831,('Nematostella vectensis Lhx3/4-like':0.919274,('Branchiostoma floridae Lhx3/4':0.061432,(('Tribolium castaneum Lhx3/4':0.038664,'Drosophila melanogaster Lhx3/4':0.086482)100:0.122709,((('Ciona intestinalis Lhx3/4':0.168703,'Mnemiopsis leidyi Lhx3/4':0.284012)52:0.076526,('Saccoglossus kowalevskii Lhx3/4':0.069443,'Amphimedon queenslandica Lhx3/4':0.262141)40:0.035657)13:0.013767,('Lottia gigantea Lhx3/4':0.169704,((Mus_musculus_Lhx4:0.037639,Danio_rerio_Lhx4:0.04334)96:0.052248,(Danio_rerio_Lhx3:0.03077,Mus_musculus_Lhx3:0.069887)74:0.027759)80:0.06934)33:0.030057)26:0.033624)40:0.039383)66:0.103636)39:0.071614)44:0.16462)54:0.106064)38:0.2036)87:0.253515)58:0.109425)90:0.212715)70:0.15372)32:0.058381)37:0.038785)58:0.075236)30:0.069878)100:0.528616);
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr76764]


END;