#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 20, 2025; 9:15 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 22817 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep22817;
        DIMENSIONS NTAX=47;
        TAXLABELS
            'A.queenslandica_crb'
            A.vastus
            'AnophelesD_Crb'
            'Apis_Crb_iso1'
            'Aplysia_Crb'
            'C.elegans_CRB1'
            'C.elegans_CRB3'
            'Caw_Crb1'
            'Caw_Crb2'
            'Chimpanzee_Crb1'
            'Chimpanzee_Crb2'
            'Danio_Crb1'
            'Danio_Crb2'
            'Danio_Crb3'
            'Daphnia_Crb'
            'Dog_Crb1'
            'Fruitfly_CrbB'
            'Gallus_Crb1'
            'Gallus_Crb2_iso12'
            'HUMAN_CRUM1'
            'HUMAN_CRUM2'
            'HUMAN_CRUM3'
            'MOUSE_CRUM1'
            'MOUSE_CRUM2'
            'MOUSE_CRUM3'
            'Macaca_Crb1'
            'Macaca_Crb2'
            'Macaca_Crb3'
            'Nasonia_Crb-iso1'
            'Nematostella_CrbA'
            'Nematostella_CrbB'
            'O.lobularis_crb'
            O.minuta
            'Opossum_Crb1'
            'Opossum_Crb2'
            'Opossum_Crb3'
            'S.ciliatum_crb'
            'Saccoglossus_CrbL'
            'Takifugu_Crb1'
            'Takifugu_Crb2'
            'Tribolium_Crb'
            'Trichoplax_CrbA'
            'Trichoplax_CrbB'
            'Urchin_Crb1'
            'Xenopus_Crb1'
            'Xenopus_Crb2'
            'Xenopus_Crb3'
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M45621]

	TITLE Character_Matrix_figure_5_tree;
	LINK TAXA = TaxaForAnalysisStep22817;
	DIMENSIONS NCHAR=71;
	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 ]
[                                .         .         .         .         .         .         . ]
'A.queenslandica_crb'   LSIII-LAVVVFVLLLFLVVVV-VVV--GLRIVRRKSRRKGFYSPAAVERESE-----GTGGQRTDRERLL
A.vastus                LIGVV-LLIVITVVLIIALVVLWKYV--------SSYYRYDKYSPAKTEVQKG-SLGLIDI---ESEETLI
'AnophelesD_Crb'        IALIV-VPVVIGILTIAGALIG---T--FLVMARNKRATRGTYSPSAQEYCNP-RLEMDNVLKPPPEERLI
'Apis_Crb_iso1'         IAVIV-GPIVGCLFIIAAGSLV---A--LFMMARKKRATRGTYSPSAQEFSNP-RVEMDNVMKPPPEERLI
'Aplysia_Crb'           -ILIL-VPILGGLLFIALIVGA--IW--LLKSWREKRASHGVYSPSQQESSGS-RVELGNVLKKPPEERLI
'C.elegans_CRB1'        ISYLF-GPIIAVVIVFAILGCL---L--LFFVIRGNNAMHGHYSPSSHEFTQN-RMAMPTVIKLPPQERLI
'C.elegans_CRB3'        IAGIV-IAVVIGVLLIGVVGFF------AFKYVKDRRKNHGEYRPQFEEQHHA---KDLPYLQPPNVEGLI
'Caw_Crb1'              VFTTI-GSVTLALLLILFLAVV------ASVLASNKRATQGSYSPSRQEKDSS-RVEMWSVMDAPAAERLI
'Caw_Crb2'              LLEVA-VPAACACLLLLLLGLL---S--GILAARKRRQSEGTYSPSQQEVAGA-RLEMDSVLKVPPEERLI
'Chimpanzee_Crb1'       IFTTI-GSVTIALLLILLLAIV------ASVVTSNKRATQGTYSPSRQEKEGS-RVEMWNLMPAPAMERLI
'Chimpanzee_Crb2'       LLEVA-VPAACACLLLLLLGLL---S--GILAARKRRQSEGTYSPSQQEVAGA-RLEMDSVLKVPPEERLI
'Danio_Crb1'            LLLSI-SLVCVVLLLVVFGVTT------ALVIALNRRATRGTYSPSRQEKEGS-RVEMWNIVQPPPMERLI
'Danio_Crb2'            WLAIA-VPLACGCILLVAIGLI---F--MLMTARKKRQSEGTYSPSHQEVAGA-RLEMDSMLKVPPEERLI
'Danio_Crb3'            VAIVV-PTVVLGLLAILTAVLV---F--LFCVVKKKRQTEGTYRPSAEEQTGARSVEAPDALKLPKEERLI
'Daphnia_Crb'           LVAII-VPIVAALLLIALVGFV---V--FVMMARNKRATRGTYSPSRQEMFSP-RVEMGQVMKPPPEERLI
'Dog_Crb1'              VFTTI-GSVTTVLLLILFLAVV------ASVVASNKRATQGTYSPSRQEKEGS-RVEMWSMRPPPALERLI
'Fruitfly_CrbB'         IAIIV-IPVVVVLLLIAGALLG---T--FLVMARNKRATRGTYSPSAQEYCNP-RLEMDNVLKPPPEERLI
'Gallus_Crb1'           VFTSL-GSVTLA-LLILFLAVV------VSVIAANKRSTQGTYSPSRQEKDGA-RVEMWSMVQPPPIERLI
'Gallus_Crb2_iso12'     LIEVA-VPVACGSLLLLSIGLI---F--MILTARKRRQSEGTYSPSQQEVAGA-RLEMDSVLKVPPEERLI
'HUMAN_CRUM1'           IFTTI-GSVTVALLLILLLAIV------ASVVTSNKRATQGTYSPSRQEKEGS-RVEMWNLMPPPAMERLI
'HUMAN_CRUM2'           LLEVA-VPAACACLLLLLLGLL---S--GILAARKRRQSEGTYSPSQQEVAGA-RLEMDSVLKVPPEERLI
'HUMAN_CRUM3'           TAIIV-VFSLLAAL-LLAVGLA---L--LVRKLREKRQTEGTYRPSSEEQVGA-RVPPTPNLKLPPEERLI
'MOUSE_CRUM1'           IFTAV-GSGTLALFFILLLAGV------ASLIASNKRATQGTYSPSGQEKAGP-RVEMWIRMPPPALERLI
'MOUSE_CRUM2'           LLEVA-VPAACACLLLLLLGLL---S--GILAARKRRQSEGTYSPSQQEVAGA-RLEMDSVLKVPPEERLI
'MOUSE_CRUM3'           VAITV-VFSILGVL-LIAVGLF---L--LMRKLREKRQTEGTYRPSSEEQVGA-RAPPPPNLKLPPEERLI
'Macaca_Crb1'           IFTAI-GSVTLALLLILLLAIV------ASVVTSNKRATQGTYSPSRQEKEGS-RVEMWNLMPPPAMERLI
'Macaca_Crb2'           LLEVA-VPAACACLLLLLLGLL---S--GILAARKRRQSEGTYSPSQQEVAGA-RLEMDSVLKVPPEERLI
'Macaca_Crb3'           TAIIV-VFSILAIL-LLAVGLA---L--LVWKLREKRQTEGTYRPSSEEQVGA-RVPPTPNLKLPPEERLI
'Nasonia_Crb-iso1'      IAVIV-GPIVGILFLIAAGSLI---A--LFMMARKKRATRGTYSPSAQEFSNP-RVEMDNVMKPPPEERLI
'Nematostella_CrbA'     DVELG-LSIAFVLVVLIVALVI---L--YFYFRKKAAKESGKYYPSEEEYKGGYPMSPLDFDKLDKEEQLL
'Nematostella_CrbB'     -EMII-IGVVVGCVALILLVLL--------IVLLMKRASNGTYSPSKEEFGGG-RVELDSMMKKPNEERLI
'O.lobularis_crb'       IAGIV-IGIVVFLILLLLLVLL----------LVRRRQHSGAYSPTETELAIG---NLLAEQERDPPEKLI
O.minuta                ----I-SILSVCLILIAILAILIAVISCYYSCRYWKSRKYNEYSPAETEVYKK-AAGLIDI---ESEETLI
'Opossum_Crb1'          IFTAI-GSITLAVLLILFLAVV------ASFIASNKRANQGTYSPSRQEKEGS-RVEMWNMVQPPPMERLI
'Opossum_Crb2'          LIEVV-VPVACGCLLLLLIGLL---S--GVLAARKRRQSEGTYSPSQQEVAGA-RLEMDSVLKVPPEERLI
'Opossum_Crb3'          TTIIY-ISSVLCIL-LLATLFL---F--LGQRLLDKRKCSGTYRPSDEEQVGD-CIPRQS-GKEPPKERLI
'S.ciliatum_crb'        TTTIV-IIVVVVVVVLLILLVL---M--GLYRRKQRGKLSGSYSPSSVEGNGA-DLDDLDV----EEERLI
'Saccoglossus_CrbL'     -VIII-GAALGGLVFIMLIILL---V--FLFSVRSKRATRGTYSPSRQEMTGS-RVEMGNVLKPPPEERLI
'Takifugu_Crb1'         -LLSV-SLVSVLLLVALVLTSV------GLAAALGRRATHGTYSPSRQEKEGS-RVEMWSITQTPPRERLI
'Takifugu_Crb2'         WLVVA-IPLTTLCMLLAILVVF---F--LIMTARKKRQSEGTYSPSSQEVAGA-RLEMGSVLKVPPEERLI
'Tribolium_Crb'         ILYII-IPIVLILSVGIAIGLA---V--LVNVARSKRATRGTYSPSAQEFCNP-RVELDHVLKPPPEERLI
'Trichoplax_CrbA'       AVAIA-VPILLVIIIIVVAIVI---F--RFYYKPRARKATGKYRPRETEQGSP-----MSTLESEGADRLI
'Trichoplax_CrbB'       -VGAT-IGIAMGVTGFILIVII---I--VVYVVIKNRAKQGRFNPSKQEEFG--RFHMADMSKLPPRERLI
'Urchin_Crb1'           WIIIG-ASLAAAVVLIIVIILL--SF--FVCSVRKKRATQGSYSPSRQEMTGS-FVEMDNVLKMPPEERLI
'Xenopus_Crb1'          VFTAV-ASVVLALFFIVCAGLC------IFIAISGMRSSQGAYSPSRQEKESS-RVEMWNIVQPPPLERLI
'Xenopus_Crb2'          ASTLVGSAIGTGMLFILLSVIT---A--VLVTMRNKRATQGTYSPSRQEKDGA-RVEMWNVLKLPPTERLI
'Xenopus_Crb3'          AAIIV-PCVVGGL--ILIGILA---F--IIIKIRERRRTEGTYRPSSEEHKEP-RVEPNMALKLPPEERLI
;
END;

[ The following blocks are output data for analysis step 22817 ]
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_5;
      LINK TAXA = TaxaForAnalysisStep22817;
      TREE 'Tree 17 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('C.elegans_CRB1',((('Nematostella_CrbB',(((O.minuta,A.vastus),'A.queenslandica_crb'),'O.lobularis_crb')),'Trichoplax_CrbB'),'Tribolium_Crb')),('Danio_Crb3',(('Xenopus_Crb3',('Trichoplax_CrbA','Nematostella_CrbA')),('C.elegans_CRB3',(('Opossum_Crb3','S.ciliatum_crb'),(('Macaca_Crb3','HUMAN_CRUM3'),'MOUSE_CRUM3')))))),(('AnophelesD_Crb','Fruitfly_CrbB'),((((('Xenopus_Crb2',('Danio_Crb1',(((('Gallus_Crb1',('Dog_Crb1',((('Chimpanzee_Crb1','Macaca_Crb1'),'HUMAN_CRUM1'),'Caw_Crb1'))),'Opossum_Crb1'),('MOUSE_CRUM1','Xenopus_Crb1')),'Takifugu_Crb1'))),'Aplysia_Crb'),(((((('Caw_Crb2',(('Chimpanzee_Crb2','HUMAN_CRUM2'),('Macaca_Crb2','MOUSE_CRUM2'))),'Opossum_Crb2'),'Gallus_Crb2_iso12'),'Takifugu_Crb2'),'Danio_Crb2'),'Urchin_Crb1')),'Saccoglossus_CrbL'),'Daphnia_Crb'))),'Nasonia_Crb-iso1'),'Apis_Crb_iso1');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111388]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_5;
      LINK TAXA = TaxaForAnalysisStep22817;
      TREE 'Tree 19 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('C.elegans_CRB1',((('Nematostella_CrbB',(((O.minuta,A.vastus),'A.queenslandica_crb'),'O.lobularis_crb')),'Trichoplax_CrbB'),'Tribolium_Crb')),('Danio_Crb3',(('Xenopus_Crb3',('Trichoplax_CrbA','Nematostella_CrbA')),('C.elegans_CRB3',(('Opossum_Crb3','S.ciliatum_crb'),(('Macaca_Crb3','HUMAN_CRUM3'),'MOUSE_CRUM3')))))),(('AnophelesD_Crb','Fruitfly_CrbB'),((((('Xenopus_Crb2',('Danio_Crb1',(((('Gallus_Crb1',('Dog_Crb1',((('Chimpanzee_Crb1','Macaca_Crb1'),'HUMAN_CRUM1'),'Caw_Crb1'))),'Opossum_Crb1'),('MOUSE_CRUM1','Xenopus_Crb1')),'Takifugu_Crb1'))),'Aplysia_Crb'),(((((('Caw_Crb2',('Chimpanzee_Crb2',(('Macaca_Crb2','HUMAN_CRUM2'),'MOUSE_CRUM2'))),'Opossum_Crb2'),'Gallus_Crb2_iso12'),'Takifugu_Crb2'),'Danio_Crb2'),'Urchin_Crb1')),'Saccoglossus_CrbL'),'Daphnia_Crb'))),'Nasonia_Crb-iso1'),'Apis_Crb_iso1');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111390]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_5;
      LINK TAXA = TaxaForAnalysisStep22817;
      TREE 'Tree 1 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('C.elegans_CRB1',((('Nematostella_CrbB',(((O.minuta,A.vastus),'A.queenslandica_crb'),'O.lobularis_crb')),'Trichoplax_CrbB'),'Tribolium_Crb')),('Danio_Crb3',(('Xenopus_Crb3',('Trichoplax_CrbA','Nematostella_CrbA')),('C.elegans_CRB3',(('Opossum_Crb3','S.ciliatum_crb'),(('Macaca_Crb3','HUMAN_CRUM3'),'MOUSE_CRUM3')))))),(('AnophelesD_Crb','Fruitfly_CrbB'),((((('Xenopus_Crb2',('Danio_Crb1',(((('Gallus_Crb1',('Dog_Crb1',((('Chimpanzee_Crb1','Macaca_Crb1'),'HUMAN_CRUM1'),'Caw_Crb1'))),'Opossum_Crb1'),('MOUSE_CRUM1','Xenopus_Crb1')),'Takifugu_Crb1'))),'Aplysia_Crb'),(((((('Caw_Crb2',('HUMAN_CRUM2',('Chimpanzee_Crb2',('Macaca_Crb2','MOUSE_CRUM2')))),'Opossum_Crb2'),'Gallus_Crb2_iso12'),'Takifugu_Crb2'),'Danio_Crb2'),'Urchin_Crb1')),'Saccoglossus_CrbL'),'Daphnia_Crb'))),'Nasonia_Crb-iso1'),'Apis_Crb_iso1');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111372]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_5;
      LINK TAXA = TaxaForAnalysisStep22817;
      TREE 'Tree 2 from search (criterion: minimize Tree value using character matrix)' = [&R] (('Nasonia_Crb-iso1','Apis_Crb_iso1'),((('C.elegans_CRB1',((('Nematostella_CrbB',(((O.minuta,A.vastus),'A.queenslandica_crb'),'O.lobularis_crb')),'Trichoplax_CrbB'),'Tribolium_Crb')),('Danio_Crb3',(('Xenopus_Crb3',('Trichoplax_CrbA','Nematostella_CrbA')),('C.elegans_CRB3',(('Opossum_Crb3','S.ciliatum_crb'),(('Macaca_Crb3','HUMAN_CRUM3'),'MOUSE_CRUM3')))))),(('AnophelesD_Crb','Fruitfly_CrbB'),((((('Xenopus_Crb2',('Danio_Crb1',(((('Gallus_Crb1',('Dog_Crb1',((('Chimpanzee_Crb1','Macaca_Crb1'),'HUMAN_CRUM1'),'Caw_Crb1'))),'Opossum_Crb1'),('MOUSE_CRUM1','Xenopus_Crb1')),'Takifugu_Crb1'))),'Aplysia_Crb'),(((((('Caw_Crb2',('HUMAN_CRUM2',('Chimpanzee_Crb2',('Macaca_Crb2','MOUSE_CRUM2')))),'Opossum_Crb2'),'Gallus_Crb2_iso12'),'Takifugu_Crb2'),'Danio_Crb2'),'Urchin_Crb1')),'Saccoglossus_CrbL'),'Daphnia_Crb'))));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111373]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_5;
      LINK TAXA = TaxaForAnalysisStep22817;
      TREE 'Tree 12 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('C.elegans_CRB1',((('Nematostella_CrbB',(((O.minuta,A.vastus),'A.queenslandica_crb'),'O.lobularis_crb')),'Trichoplax_CrbB'),'Tribolium_Crb')),('Danio_Crb3',(('Xenopus_Crb3',('Trichoplax_CrbA','Nematostella_CrbA')),('C.elegans_CRB3',(('Opossum_Crb3','S.ciliatum_crb'),(('Macaca_Crb3','HUMAN_CRUM3'),'MOUSE_CRUM3')))))),(('AnophelesD_Crb','Fruitfly_CrbB'),((((('Xenopus_Crb2',('Danio_Crb1',(((('Gallus_Crb1',('Dog_Crb1',((('Chimpanzee_Crb1','Macaca_Crb1'),'HUMAN_CRUM1'),'Caw_Crb1'))),'Opossum_Crb1'),('MOUSE_CRUM1','Xenopus_Crb1')),'Takifugu_Crb1'))),'Aplysia_Crb'),(((((('HUMAN_CRUM2',('Caw_Crb2',('Chimpanzee_Crb2',('Macaca_Crb2','MOUSE_CRUM2')))),'Opossum_Crb2'),'Gallus_Crb2_iso12'),'Takifugu_Crb2'),'Danio_Crb2'),'Urchin_Crb1')),'Saccoglossus_CrbL'),'Daphnia_Crb'))),'Nasonia_Crb-iso1'),'Apis_Crb_iso1');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111383]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_5;
      LINK TAXA = TaxaForAnalysisStep22817;
      TREE 'Tree 26 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('C.elegans_CRB1',((('Nematostella_CrbB',(((O.minuta,A.vastus),'A.queenslandica_crb'),'O.lobularis_crb')),'Trichoplax_CrbB'),'Tribolium_Crb')),('Danio_Crb3',(('Xenopus_Crb3',('Trichoplax_CrbA','Nematostella_CrbA')),('C.elegans_CRB3',(('Opossum_Crb3','S.ciliatum_crb'),(('Macaca_Crb3','HUMAN_CRUM3'),'MOUSE_CRUM3')))))),(('AnophelesD_Crb','Fruitfly_CrbB'),((((('Xenopus_Crb2',('Danio_Crb1',(((('Gallus_Crb1',('Dog_Crb1',((('Chimpanzee_Crb1','Macaca_Crb1'),'HUMAN_CRUM1'),'Caw_Crb1'))),'Opossum_Crb1'),('MOUSE_CRUM1','Xenopus_Crb1')),'Takifugu_Crb1'))),'Aplysia_Crb'),((((((('Caw_Crb2',('Macaca_Crb2','MOUSE_CRUM2')),('HUMAN_CRUM2','Chimpanzee_Crb2')),'Opossum_Crb2'),'Gallus_Crb2_iso12'),'Takifugu_Crb2'),'Danio_Crb2'),'Urchin_Crb1')),'Saccoglossus_CrbL'),'Daphnia_Crb'))),'Nasonia_Crb-iso1'),'Apis_Crb_iso1');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111397]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_5;
      LINK TAXA = TaxaForAnalysisStep22817;
      TREE 'Tree 100 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('C.elegans_CRB1',(((((O.minuta,A.vastus),'A.queenslandica_crb'),('Nematostella_CrbB','O.lobularis_crb')),'Trichoplax_CrbB'),'Tribolium_Crb')),('Danio_Crb3',(('Xenopus_Crb3',('Trichoplax_CrbA','Nematostella_CrbA')),('C.elegans_CRB3',(('Opossum_Crb3','S.ciliatum_crb'),(('Macaca_Crb3','HUMAN_CRUM3'),'MOUSE_CRUM3')))))),(('AnophelesD_Crb','Fruitfly_CrbB'),((((('Xenopus_Crb2',(((('Gallus_Crb1',('Dog_Crb1',((('Chimpanzee_Crb1','Macaca_Crb1'),'HUMAN_CRUM1'),'Caw_Crb1'))),'Opossum_Crb1'),('MOUSE_CRUM1','Xenopus_Crb1')),('Danio_Crb1','Takifugu_Crb1'))),'Aplysia_Crb'),(((((('Caw_Crb2',('HUMAN_CRUM2',('Chimpanzee_Crb2',('Macaca_Crb2','MOUSE_CRUM2')))),'Opossum_Crb2'),'Gallus_Crb2_iso12'),'Takifugu_Crb2'),'Danio_Crb2'),'Urchin_Crb1')),'Saccoglossus_CrbL'),'Daphnia_Crb'))),'Nasonia_Crb-iso1'),'Apis_Crb_iso1');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111401]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_5;
      LINK TAXA = TaxaForAnalysisStep22817;
      TREE 'Tree 8 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('C.elegans_CRB1',((('Nematostella_CrbB',(((O.minuta,A.vastus),'A.queenslandica_crb'),'O.lobularis_crb')),'Trichoplax_CrbB'),'Tribolium_Crb')),('Danio_Crb3',(('Xenopus_Crb3',('Trichoplax_CrbA','Nematostella_CrbA')),('C.elegans_CRB3',(('Opossum_Crb3','S.ciliatum_crb'),(('Macaca_Crb3','HUMAN_CRUM3'),'MOUSE_CRUM3')))))),(('AnophelesD_Crb','Fruitfly_CrbB'),((((('Xenopus_Crb2',('Danio_Crb1',(((('Gallus_Crb1',((('Chimpanzee_Crb1','Macaca_Crb1'),'HUMAN_CRUM1'),('Dog_Crb1','Caw_Crb1'))),'Opossum_Crb1'),('MOUSE_CRUM1','Xenopus_Crb1')),'Takifugu_Crb1'))),'Aplysia_Crb'),(((((('Caw_Crb2',('HUMAN_CRUM2',('Chimpanzee_Crb2',('Macaca_Crb2','MOUSE_CRUM2')))),'Opossum_Crb2'),'Gallus_Crb2_iso12'),'Takifugu_Crb2'),'Danio_Crb2'),'Urchin_Crb1')),'Saccoglossus_CrbL'),'Daphnia_Crb'))),'Nasonia_Crb-iso1'),'Apis_Crb_iso1');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111379]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_5;
      LINK TAXA = TaxaForAnalysisStep22817;
      TREE 'Tree 27 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('C.elegans_CRB1',((('Nematostella_CrbB',(((O.minuta,A.vastus),'A.queenslandica_crb'),'O.lobularis_crb')),'Trichoplax_CrbB'),'Tribolium_Crb')),('Danio_Crb3',(('Xenopus_Crb3',('Trichoplax_CrbA','Nematostella_CrbA')),('C.elegans_CRB3',(('Opossum_Crb3','S.ciliatum_crb'),(('Macaca_Crb3','HUMAN_CRUM3'),'MOUSE_CRUM3')))))),(('AnophelesD_Crb','Fruitfly_CrbB'),((((('Xenopus_Crb2',('Danio_Crb1',(((('Gallus_Crb1',('Dog_Crb1',((('Chimpanzee_Crb1','Macaca_Crb1'),'HUMAN_CRUM1'),'Caw_Crb1'))),'Opossum_Crb1'),('MOUSE_CRUM1','Xenopus_Crb1')),'Takifugu_Crb1'))),'Aplysia_Crb'),((((((('Caw_Crb2',('HUMAN_CRUM2',('Chimpanzee_Crb2','MOUSE_CRUM2'))),'Macaca_Crb2'),'Opossum_Crb2'),'Gallus_Crb2_iso12'),'Takifugu_Crb2'),'Danio_Crb2'),'Urchin_Crb1')),'Saccoglossus_CrbL'),'Daphnia_Crb'))),'Nasonia_Crb-iso1'),'Apis_Crb_iso1');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111398]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_5;
      LINK TAXA = TaxaForAnalysisStep22817;
      TREE 'Tree 7 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('C.elegans_CRB1',((('Nematostella_CrbB',(((O.minuta,A.vastus),'A.queenslandica_crb'),'O.lobularis_crb')),'Trichoplax_CrbB'),'Tribolium_Crb')),('Danio_Crb3',(('Xenopus_Crb3',('Trichoplax_CrbA','Nematostella_CrbA')),('C.elegans_CRB3',(('Opossum_Crb3','S.ciliatum_crb'),(('Macaca_Crb3','HUMAN_CRUM3'),'MOUSE_CRUM3')))))),(('AnophelesD_Crb','Fruitfly_CrbB'),((((('Xenopus_Crb2',('Danio_Crb1',(((('Gallus_Crb1',(((('Chimpanzee_Crb1','Macaca_Crb1'),'HUMAN_CRUM1'),'Dog_Crb1'),'Caw_Crb1')),'Opossum_Crb1'),('MOUSE_CRUM1','Xenopus_Crb1')),'Takifugu_Crb1'))),'Aplysia_Crb'),(((((('Caw_Crb2',('HUMAN_CRUM2',('Chimpanzee_Crb2',('Macaca_Crb2','MOUSE_CRUM2')))),'Opossum_Crb2'),'Gallus_Crb2_iso12'),'Takifugu_Crb2'),'Danio_Crb2'),'Urchin_Crb1')),'Saccoglossus_CrbL'),'Daphnia_Crb'))),'Nasonia_Crb-iso1'),'Apis_Crb_iso1');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111378]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_5;
      LINK TAXA = TaxaForAnalysisStep22817;
      TREE 'Tree 23 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('C.elegans_CRB1',((('Nematostella_CrbB',(((O.minuta,A.vastus),'A.queenslandica_crb'),'O.lobularis_crb')),'Trichoplax_CrbB'),'Tribolium_Crb')),('Danio_Crb3',(('Xenopus_Crb3',('Trichoplax_CrbA','Nematostella_CrbA')),('C.elegans_CRB3',(('Opossum_Crb3','S.ciliatum_crb'),(('Macaca_Crb3','HUMAN_CRUM3'),'MOUSE_CRUM3')))))),(('AnophelesD_Crb','Fruitfly_CrbB'),((((('Xenopus_Crb2',('Danio_Crb1',(((('Gallus_Crb1',('Dog_Crb1',((('Chimpanzee_Crb1','Macaca_Crb1'),'HUMAN_CRUM1'),'Caw_Crb1'))),'Opossum_Crb1'),('MOUSE_CRUM1','Xenopus_Crb1')),'Takifugu_Crb1'))),'Aplysia_Crb'),(((((('Caw_Crb2',('HUMAN_CRUM2',(('Macaca_Crb2','Chimpanzee_Crb2'),'MOUSE_CRUM2'))),'Opossum_Crb2'),'Gallus_Crb2_iso12'),'Takifugu_Crb2'),'Danio_Crb2'),'Urchin_Crb1')),'Saccoglossus_CrbL'),'Daphnia_Crb'))),'Nasonia_Crb-iso1'),'Apis_Crb_iso1');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111394]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_5;
      LINK TAXA = TaxaForAnalysisStep22817;
      TREE 'Tree 4 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('C.elegans_CRB1',(((((O.minuta,A.vastus),'A.queenslandica_crb'),('Nematostella_CrbB','O.lobularis_crb')),'Trichoplax_CrbB'),'Tribolium_Crb')),('Danio_Crb3',(('Xenopus_Crb3',('Trichoplax_CrbA','Nematostella_CrbA')),('C.elegans_CRB3',(('Opossum_Crb3','S.ciliatum_crb'),(('Macaca_Crb3','HUMAN_CRUM3'),'MOUSE_CRUM3')))))),(('AnophelesD_Crb','Fruitfly_CrbB'),((((('Xenopus_Crb2',('Danio_Crb1',(((('Gallus_Crb1',('Dog_Crb1',((('Chimpanzee_Crb1','Macaca_Crb1'),'HUMAN_CRUM1'),'Caw_Crb1'))),'Opossum_Crb1'),('MOUSE_CRUM1','Xenopus_Crb1')),'Takifugu_Crb1'))),'Aplysia_Crb'),(((((('Caw_Crb2',('HUMAN_CRUM2',('Chimpanzee_Crb2',('Macaca_Crb2','MOUSE_CRUM2')))),'Opossum_Crb2'),'Gallus_Crb2_iso12'),'Takifugu_Crb2'),'Danio_Crb2'),'Urchin_Crb1')),'Saccoglossus_CrbL'),'Daphnia_Crb'))),'Nasonia_Crb-iso1'),'Apis_Crb_iso1');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111375]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_5;
      LINK TAXA = TaxaForAnalysisStep22817;
      TREE 'Tree 16 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('C.elegans_CRB1',((('Nematostella_CrbB',(((O.minuta,A.vastus),'A.queenslandica_crb'),'O.lobularis_crb')),'Trichoplax_CrbB'),'Tribolium_Crb')),('Danio_Crb3',(('Xenopus_Crb3',('Trichoplax_CrbA','Nematostella_CrbA')),('C.elegans_CRB3',(('Opossum_Crb3','S.ciliatum_crb'),(('Macaca_Crb3','HUMAN_CRUM3'),'MOUSE_CRUM3')))))),(('AnophelesD_Crb','Fruitfly_CrbB'),((((('Xenopus_Crb2',('Danio_Crb1',(((('Gallus_Crb1',('Dog_Crb1',((('Chimpanzee_Crb1','Macaca_Crb1'),'HUMAN_CRUM1'),'Caw_Crb1'))),'Opossum_Crb1'),('MOUSE_CRUM1','Xenopus_Crb1')),'Takifugu_Crb1'))),'Aplysia_Crb'),(((((('HUMAN_CRUM2',('Chimpanzee_Crb2',('Macaca_Crb2',('Caw_Crb2','MOUSE_CRUM2')))),'Opossum_Crb2'),'Gallus_Crb2_iso12'),'Takifugu_Crb2'),'Danio_Crb2'),'Urchin_Crb1')),'Saccoglossus_CrbL'),'Daphnia_Crb'))),'Nasonia_Crb-iso1'),'Apis_Crb_iso1');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111387]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_5;
      LINK TAXA = TaxaForAnalysisStep22817;
      TREE 'Tree 21 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('C.elegans_CRB1',((('Nematostella_CrbB',(((O.minuta,A.vastus),'A.queenslandica_crb'),'O.lobularis_crb')),'Trichoplax_CrbB'),'Tribolium_Crb')),('Danio_Crb3',(('Xenopus_Crb3',('Trichoplax_CrbA','Nematostella_CrbA')),('C.elegans_CRB3',(('Opossum_Crb3','S.ciliatum_crb'),(('Macaca_Crb3','HUMAN_CRUM3'),'MOUSE_CRUM3')))))),(('AnophelesD_Crb','Fruitfly_CrbB'),((((('Xenopus_Crb2',('Danio_Crb1',(((('Gallus_Crb1',('Dog_Crb1',((('Chimpanzee_Crb1','Macaca_Crb1'),'HUMAN_CRUM1'),'Caw_Crb1'))),'Opossum_Crb1'),('MOUSE_CRUM1','Xenopus_Crb1')),'Takifugu_Crb1'))),'Aplysia_Crb'),((((((('Caw_Crb2',('HUMAN_CRUM2',('Macaca_Crb2','MOUSE_CRUM2'))),'Chimpanzee_Crb2'),'Opossum_Crb2'),'Gallus_Crb2_iso12'),'Takifugu_Crb2'),'Danio_Crb2'),'Urchin_Crb1')),'Saccoglossus_CrbL'),'Daphnia_Crb'))),'Nasonia_Crb-iso1'),'Apis_Crb_iso1');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111392]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_5;
      LINK TAXA = TaxaForAnalysisStep22817;
      TREE 'Tree 28 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('C.elegans_CRB1',((('Nematostella_CrbB',(((O.minuta,A.vastus),'A.queenslandica_crb'),'O.lobularis_crb')),'Trichoplax_CrbB'),'Tribolium_Crb')),('Danio_Crb3',(('Xenopus_Crb3',('Trichoplax_CrbA','Nematostella_CrbA')),('C.elegans_CRB3',(('Opossum_Crb3','S.ciliatum_crb'),(('Macaca_Crb3','HUMAN_CRUM3'),'MOUSE_CRUM3')))))),(('AnophelesD_Crb','Fruitfly_CrbB'),((((('Xenopus_Crb2',('Danio_Crb1',(((('Gallus_Crb1',('Dog_Crb1',((('Chimpanzee_Crb1','Macaca_Crb1'),'HUMAN_CRUM1'),'Caw_Crb1'))),'Opossum_Crb1'),('MOUSE_CRUM1','Xenopus_Crb1')),'Takifugu_Crb1'))),'Aplysia_Crb'),((((((('Caw_Crb2','Macaca_Crb2'),('HUMAN_CRUM2',('Chimpanzee_Crb2','MOUSE_CRUM2'))),'Opossum_Crb2'),'Gallus_Crb2_iso12'),'Takifugu_Crb2'),'Danio_Crb2'),'Urchin_Crb1')),'Saccoglossus_CrbL'),'Daphnia_Crb'))),'Nasonia_Crb-iso1'),'Apis_Crb_iso1');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111399]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_5;
      LINK TAXA = TaxaForAnalysisStep22817;
      TREE 'Tree 22 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('C.elegans_CRB1',((('Nematostella_CrbB',(((O.minuta,A.vastus),'A.queenslandica_crb'),'O.lobularis_crb')),'Trichoplax_CrbB'),'Tribolium_Crb')),('Danio_Crb3',(('Xenopus_Crb3',('Trichoplax_CrbA','Nematostella_CrbA')),('C.elegans_CRB3',(('Opossum_Crb3','S.ciliatum_crb'),(('Macaca_Crb3','HUMAN_CRUM3'),'MOUSE_CRUM3')))))),(('AnophelesD_Crb','Fruitfly_CrbB'),((((('Xenopus_Crb2',('Danio_Crb1',(((('Gallus_Crb1',('Dog_Crb1',((('Chimpanzee_Crb1','Macaca_Crb1'),'HUMAN_CRUM1'),'Caw_Crb1'))),'Opossum_Crb1'),('MOUSE_CRUM1','Xenopus_Crb1')),'Takifugu_Crb1'))),'Aplysia_Crb'),((((((('Caw_Crb2','Chimpanzee_Crb2'),('HUMAN_CRUM2',('Macaca_Crb2','MOUSE_CRUM2'))),'Opossum_Crb2'),'Gallus_Crb2_iso12'),'Takifugu_Crb2'),'Danio_Crb2'),'Urchin_Crb1')),'Saccoglossus_CrbL'),'Daphnia_Crb'))),'Nasonia_Crb-iso1'),'Apis_Crb_iso1');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111393]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_5;
      LINK TAXA = TaxaForAnalysisStep22817;
      TREE 'Tree 18 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('C.elegans_CRB1',((('Nematostella_CrbB',(((O.minuta,A.vastus),'A.queenslandica_crb'),'O.lobularis_crb')),'Trichoplax_CrbB'),'Tribolium_Crb')),('Danio_Crb3',(('Xenopus_Crb3',('Trichoplax_CrbA','Nematostella_CrbA')),('C.elegans_CRB3',(('Opossum_Crb3','S.ciliatum_crb'),(('Macaca_Crb3','HUMAN_CRUM3'),'MOUSE_CRUM3')))))),(('AnophelesD_Crb','Fruitfly_CrbB'),((((('Xenopus_Crb2',('Danio_Crb1',(((('Gallus_Crb1',('Dog_Crb1',((('Chimpanzee_Crb1','Macaca_Crb1'),'HUMAN_CRUM1'),'Caw_Crb1'))),'Opossum_Crb1'),('MOUSE_CRUM1','Xenopus_Crb1')),'Takifugu_Crb1'))),'Aplysia_Crb'),(((((('Caw_Crb2',('Chimpanzee_Crb2',('HUMAN_CRUM2',('Macaca_Crb2','MOUSE_CRUM2')))),'Opossum_Crb2'),'Gallus_Crb2_iso12'),'Takifugu_Crb2'),'Danio_Crb2'),'Urchin_Crb1')),'Saccoglossus_CrbL'),'Daphnia_Crb'))),'Nasonia_Crb-iso1'),'Apis_Crb_iso1');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111389]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_5;
      LINK TAXA = TaxaForAnalysisStep22817;
      TREE 'Tree 14 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('C.elegans_CRB1',((('Nematostella_CrbB',(((O.minuta,A.vastus),'A.queenslandica_crb'),'O.lobularis_crb')),'Trichoplax_CrbB'),'Tribolium_Crb')),('Danio_Crb3',(('Xenopus_Crb3',('Trichoplax_CrbA','Nematostella_CrbA')),('C.elegans_CRB3',(('Opossum_Crb3','S.ciliatum_crb'),(('Macaca_Crb3','HUMAN_CRUM3'),'MOUSE_CRUM3')))))),(('AnophelesD_Crb','Fruitfly_CrbB'),((((('Xenopus_Crb2',('Danio_Crb1',(((('Gallus_Crb1',('Dog_Crb1',((('Chimpanzee_Crb1','Macaca_Crb1'),'HUMAN_CRUM1'),'Caw_Crb1'))),'Opossum_Crb1'),('MOUSE_CRUM1','Xenopus_Crb1')),'Takifugu_Crb1'))),'Aplysia_Crb'),(((((('HUMAN_CRUM2',('Chimpanzee_Crb2',('Caw_Crb2',('Macaca_Crb2','MOUSE_CRUM2')))),'Opossum_Crb2'),'Gallus_Crb2_iso12'),'Takifugu_Crb2'),'Danio_Crb2'),'Urchin_Crb1')),'Saccoglossus_CrbL'),'Daphnia_Crb'))),'Nasonia_Crb-iso1'),'Apis_Crb_iso1');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111385]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_5;
      LINK TAXA = TaxaForAnalysisStep22817;
      TREE 'Tree 6 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('C.elegans_CRB1',((('Nematostella_CrbB',(((O.minuta,A.vastus),'A.queenslandica_crb'),'O.lobularis_crb')),'Trichoplax_CrbB'),'Tribolium_Crb')),('Danio_Crb3',(('Xenopus_Crb3',('Trichoplax_CrbA','Nematostella_CrbA')),('C.elegans_CRB3',(('Opossum_Crb3','S.ciliatum_crb'),(('Macaca_Crb3','HUMAN_CRUM3'),'MOUSE_CRUM3')))))),(('AnophelesD_Crb','Fruitfly_CrbB'),((((('Xenopus_Crb2',(((('Gallus_Crb1',('Dog_Crb1',((('Chimpanzee_Crb1','Macaca_Crb1'),'HUMAN_CRUM1'),'Caw_Crb1'))),'Opossum_Crb1'),('MOUSE_CRUM1','Xenopus_Crb1')),('Danio_Crb1','Takifugu_Crb1'))),'Aplysia_Crb'),(((((('Caw_Crb2',('HUMAN_CRUM2',('Chimpanzee_Crb2',('Macaca_Crb2','MOUSE_CRUM2')))),'Opossum_Crb2'),'Gallus_Crb2_iso12'),'Takifugu_Crb2'),'Danio_Crb2'),'Urchin_Crb1')),'Saccoglossus_CrbL'),'Daphnia_Crb'))),'Nasonia_Crb-iso1'),'Apis_Crb_iso1');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111377]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_5;
      LINK TAXA = TaxaForAnalysisStep22817;
      TREE 'Tree 5 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('C.elegans_CRB1',((('Nematostella_CrbB',(((A.vastus,'A.queenslandica_crb'),O.minuta),'O.lobularis_crb')),'Trichoplax_CrbB'),'Tribolium_Crb')),('Danio_Crb3',(('Xenopus_Crb3',('Trichoplax_CrbA','Nematostella_CrbA')),('C.elegans_CRB3',(('Opossum_Crb3','S.ciliatum_crb'),(('Macaca_Crb3','HUMAN_CRUM3'),'MOUSE_CRUM3')))))),(('AnophelesD_Crb','Fruitfly_CrbB'),((((('Xenopus_Crb2',('Danio_Crb1',(((('Gallus_Crb1',('Dog_Crb1',((('Chimpanzee_Crb1','Macaca_Crb1'),'HUMAN_CRUM1'),'Caw_Crb1'))),'Opossum_Crb1'),('MOUSE_CRUM1','Xenopus_Crb1')),'Takifugu_Crb1'))),'Aplysia_Crb'),(((((('Caw_Crb2',('HUMAN_CRUM2',('Chimpanzee_Crb2',('Macaca_Crb2','MOUSE_CRUM2')))),'Opossum_Crb2'),'Gallus_Crb2_iso12'),'Takifugu_Crb2'),'Danio_Crb2'),'Urchin_Crb1')),'Saccoglossus_CrbL'),'Daphnia_Crb'))),'Nasonia_Crb-iso1'),'Apis_Crb_iso1');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111376]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_5;
      LINK TAXA = TaxaForAnalysisStep22817;
      TREE 'Tree 9 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('C.elegans_CRB1',((('Nematostella_CrbB',(((O.minuta,A.vastus),'A.queenslandica_crb'),'O.lobularis_crb')),'Trichoplax_CrbB'),'Tribolium_Crb')),('Danio_Crb3',(('Xenopus_Crb3',('Trichoplax_CrbA','Nematostella_CrbA')),('C.elegans_CRB3',(('Opossum_Crb3','S.ciliatum_crb'),(('Macaca_Crb3','HUMAN_CRUM3'),'MOUSE_CRUM3')))))),(('AnophelesD_Crb','Fruitfly_CrbB'),((((('Xenopus_Crb2',('Danio_Crb1',(((('Gallus_Crb1',('Dog_Crb1',((('Macaca_Crb1','HUMAN_CRUM1'),'Chimpanzee_Crb1'),'Caw_Crb1'))),'Opossum_Crb1'),('MOUSE_CRUM1','Xenopus_Crb1')),'Takifugu_Crb1'))),'Aplysia_Crb'),(((((('Caw_Crb2',('HUMAN_CRUM2',('Chimpanzee_Crb2',('Macaca_Crb2','MOUSE_CRUM2')))),'Opossum_Crb2'),'Gallus_Crb2_iso12'),'Takifugu_Crb2'),'Danio_Crb2'),'Urchin_Crb1')),'Saccoglossus_CrbL'),'Daphnia_Crb'))),'Nasonia_Crb-iso1'),'Apis_Crb_iso1');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111380]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_5;
      LINK TAXA = TaxaForAnalysisStep22817;
      TREE 'Tree 3 from search (criterion: minimize Tree value using character matrix)' = [&R] ('Nasonia_Crb-iso1',(((('C.elegans_CRB1',((('Nematostella_CrbB',(((O.minuta,A.vastus),'A.queenslandica_crb'),'O.lobularis_crb')),'Trichoplax_CrbB'),'Tribolium_Crb')),('Danio_Crb3',(('Xenopus_Crb3',('Trichoplax_CrbA','Nematostella_CrbA')),('C.elegans_CRB3',(('Opossum_Crb3','S.ciliatum_crb'),(('Macaca_Crb3','HUMAN_CRUM3'),'MOUSE_CRUM3')))))),(('AnophelesD_Crb','Fruitfly_CrbB'),((((('Xenopus_Crb2',('Danio_Crb1',(((('Gallus_Crb1',('Dog_Crb1',((('Chimpanzee_Crb1','Macaca_Crb1'),'HUMAN_CRUM1'),'Caw_Crb1'))),'Opossum_Crb1'),('MOUSE_CRUM1','Xenopus_Crb1')),'Takifugu_Crb1'))),'Aplysia_Crb'),(((((('Caw_Crb2',('HUMAN_CRUM2',('Chimpanzee_Crb2',('Macaca_Crb2','MOUSE_CRUM2')))),'Opossum_Crb2'),'Gallus_Crb2_iso12'),'Takifugu_Crb2'),'Danio_Crb2'),'Urchin_Crb1')),'Saccoglossus_CrbL'),'Daphnia_Crb'))),'Apis_Crb_iso1'));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111374]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_5;
      LINK TAXA = TaxaForAnalysisStep22817;
      TREE 'Tree 15 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('C.elegans_CRB1',((('Nematostella_CrbB',(((O.minuta,A.vastus),'A.queenslandica_crb'),'O.lobularis_crb')),'Trichoplax_CrbB'),'Tribolium_Crb')),('Danio_Crb3',(('Xenopus_Crb3',('Trichoplax_CrbA','Nematostella_CrbA')),('C.elegans_CRB3',(('Opossum_Crb3','S.ciliatum_crb'),(('Macaca_Crb3','HUMAN_CRUM3'),'MOUSE_CRUM3')))))),(('AnophelesD_Crb','Fruitfly_CrbB'),((((('Xenopus_Crb2',('Danio_Crb1',(((('Gallus_Crb1',('Dog_Crb1',((('Chimpanzee_Crb1','Macaca_Crb1'),'HUMAN_CRUM1'),'Caw_Crb1'))),'Opossum_Crb1'),('MOUSE_CRUM1','Xenopus_Crb1')),'Takifugu_Crb1'))),'Aplysia_Crb'),(((((('HUMAN_CRUM2',('Chimpanzee_Crb2',(('Macaca_Crb2','Caw_Crb2'),'MOUSE_CRUM2'))),'Opossum_Crb2'),'Gallus_Crb2_iso12'),'Takifugu_Crb2'),'Danio_Crb2'),'Urchin_Crb1')),'Saccoglossus_CrbL'),'Daphnia_Crb'))),'Nasonia_Crb-iso1'),'Apis_Crb_iso1');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111386]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_5;
      LINK TAXA = TaxaForAnalysisStep22817;
      TREE 'Tree 11 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('C.elegans_CRB1',((('Nematostella_CrbB',(((O.minuta,A.vastus),'A.queenslandica_crb'),'O.lobularis_crb')),'Trichoplax_CrbB'),'Tribolium_Crb')),('Danio_Crb3',(('Xenopus_Crb3',('Trichoplax_CrbA','Nematostella_CrbA')),('C.elegans_CRB3',(('Opossum_Crb3','S.ciliatum_crb'),(('Macaca_Crb3','HUMAN_CRUM3'),'MOUSE_CRUM3')))))),(('AnophelesD_Crb','Fruitfly_CrbB'),((((('Xenopus_Crb2',('Danio_Crb1',(((('Gallus_Crb1',('Dog_Crb1',((('Chimpanzee_Crb1','Macaca_Crb1'),'HUMAN_CRUM1'),'Caw_Crb1'))),'Opossum_Crb1'),('MOUSE_CRUM1','Xenopus_Crb1')),'Takifugu_Crb1'))),'Aplysia_Crb'),((((((('HUMAN_CRUM2','Caw_Crb2'),('Chimpanzee_Crb2',('Macaca_Crb2','MOUSE_CRUM2'))),'Opossum_Crb2'),'Gallus_Crb2_iso12'),'Takifugu_Crb2'),'Danio_Crb2'),'Urchin_Crb1')),'Saccoglossus_CrbL'),'Daphnia_Crb'))),'Nasonia_Crb-iso1'),'Apis_Crb_iso1');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111382]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_5;
      LINK TAXA = TaxaForAnalysisStep22817;
      TREE 'Tree 25 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('C.elegans_CRB1',((('Nematostella_CrbB',(((O.minuta,A.vastus),'A.queenslandica_crb'),'O.lobularis_crb')),'Trichoplax_CrbB'),'Tribolium_Crb')),('Danio_Crb3',(('Xenopus_Crb3',('Trichoplax_CrbA','Nematostella_CrbA')),('C.elegans_CRB3',(('Opossum_Crb3','S.ciliatum_crb'),(('Macaca_Crb3','HUMAN_CRUM3'),'MOUSE_CRUM3')))))),(('AnophelesD_Crb','Fruitfly_CrbB'),((((('Xenopus_Crb2',('Danio_Crb1',(((('Gallus_Crb1',('Dog_Crb1',((('Chimpanzee_Crb1','Macaca_Crb1'),'HUMAN_CRUM1'),'Caw_Crb1'))),'Opossum_Crb1'),('MOUSE_CRUM1','Xenopus_Crb1')),'Takifugu_Crb1'))),'Aplysia_Crb'),((((((('Caw_Crb2',('HUMAN_CRUM2','Chimpanzee_Crb2')),('Macaca_Crb2','MOUSE_CRUM2')),'Opossum_Crb2'),'Gallus_Crb2_iso12'),'Takifugu_Crb2'),'Danio_Crb2'),'Urchin_Crb1')),'Saccoglossus_CrbL'),'Daphnia_Crb'))),'Nasonia_Crb-iso1'),'Apis_Crb_iso1');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111396]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_5;
      LINK TAXA = TaxaForAnalysisStep22817;
      TREE 'Tree 10 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('C.elegans_CRB1',((('Nematostella_CrbB',(((O.minuta,A.vastus),'A.queenslandica_crb'),'O.lobularis_crb')),'Trichoplax_CrbB'),'Tribolium_Crb')),('Danio_Crb3',(('Xenopus_Crb3',('Trichoplax_CrbA','Nematostella_CrbA')),('C.elegans_CRB3',(('Opossum_Crb3','S.ciliatum_crb'),(('Macaca_Crb3','HUMAN_CRUM3'),'MOUSE_CRUM3')))))),(('AnophelesD_Crb','Fruitfly_CrbB'),((((('Xenopus_Crb2',('Danio_Crb1',(((('Gallus_Crb1',('Dog_Crb1',(('Macaca_Crb1',('Chimpanzee_Crb1','HUMAN_CRUM1')),'Caw_Crb1'))),'Opossum_Crb1'),('MOUSE_CRUM1','Xenopus_Crb1')),'Takifugu_Crb1'))),'Aplysia_Crb'),(((((('Caw_Crb2',('HUMAN_CRUM2',('Chimpanzee_Crb2',('Macaca_Crb2','MOUSE_CRUM2')))),'Opossum_Crb2'),'Gallus_Crb2_iso12'),'Takifugu_Crb2'),'Danio_Crb2'),'Urchin_Crb1')),'Saccoglossus_CrbL'),'Daphnia_Crb'))),'Nasonia_Crb-iso1'),'Apis_Crb_iso1');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111381]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_5;
      LINK TAXA = TaxaForAnalysisStep22817;
      TREE 'Tree 24 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('C.elegans_CRB1',((('Nematostella_CrbB',(((O.minuta,A.vastus),'A.queenslandica_crb'),'O.lobularis_crb')),'Trichoplax_CrbB'),'Tribolium_Crb')),('Danio_Crb3',(('Xenopus_Crb3',('Trichoplax_CrbA','Nematostella_CrbA')),('C.elegans_CRB3',(('Opossum_Crb3','S.ciliatum_crb'),(('Macaca_Crb3','HUMAN_CRUM3'),'MOUSE_CRUM3')))))),(('AnophelesD_Crb','Fruitfly_CrbB'),((((('Xenopus_Crb2',('Danio_Crb1',(((('Gallus_Crb1',('Dog_Crb1',((('Chimpanzee_Crb1','Macaca_Crb1'),'HUMAN_CRUM1'),'Caw_Crb1'))),'Opossum_Crb1'),('MOUSE_CRUM1','Xenopus_Crb1')),'Takifugu_Crb1'))),'Aplysia_Crb'),(((((('Caw_Crb2',('HUMAN_CRUM2',('Macaca_Crb2',('Chimpanzee_Crb2','MOUSE_CRUM2')))),'Opossum_Crb2'),'Gallus_Crb2_iso12'),'Takifugu_Crb2'),'Danio_Crb2'),'Urchin_Crb1')),'Saccoglossus_CrbL'),'Daphnia_Crb'))),'Nasonia_Crb-iso1'),'Apis_Crb_iso1');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111395]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_5;
      LINK TAXA = TaxaForAnalysisStep22817;
      TREE 'Tree 13 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('C.elegans_CRB1',((('Nematostella_CrbB',(((O.minuta,A.vastus),'A.queenslandica_crb'),'O.lobularis_crb')),'Trichoplax_CrbB'),'Tribolium_Crb')),('Danio_Crb3',(('Xenopus_Crb3',('Trichoplax_CrbA','Nematostella_CrbA')),('C.elegans_CRB3',(('Opossum_Crb3','S.ciliatum_crb'),(('Macaca_Crb3','HUMAN_CRUM3'),'MOUSE_CRUM3')))))),(('AnophelesD_Crb','Fruitfly_CrbB'),((((('Xenopus_Crb2',('Danio_Crb1',(((('Gallus_Crb1',('Dog_Crb1',((('Chimpanzee_Crb1','Macaca_Crb1'),'HUMAN_CRUM1'),'Caw_Crb1'))),'Opossum_Crb1'),('MOUSE_CRUM1','Xenopus_Crb1')),'Takifugu_Crb1'))),'Aplysia_Crb'),(((((('HUMAN_CRUM2',(('Chimpanzee_Crb2','Caw_Crb2'),('Macaca_Crb2','MOUSE_CRUM2'))),'Opossum_Crb2'),'Gallus_Crb2_iso12'),'Takifugu_Crb2'),'Danio_Crb2'),'Urchin_Crb1')),'Saccoglossus_CrbL'),'Daphnia_Crb'))),'Nasonia_Crb-iso1'),'Apis_Crb_iso1');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111384]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_5;
      LINK TAXA = TaxaForAnalysisStep22817;
      TREE 'Tree 20 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('C.elegans_CRB1',((('Nematostella_CrbB',(((O.minuta,A.vastus),'A.queenslandica_crb'),'O.lobularis_crb')),'Trichoplax_CrbB'),'Tribolium_Crb')),('Danio_Crb3',(('Xenopus_Crb3',('Trichoplax_CrbA','Nematostella_CrbA')),('C.elegans_CRB3',(('Opossum_Crb3','S.ciliatum_crb'),(('Macaca_Crb3','HUMAN_CRUM3'),'MOUSE_CRUM3')))))),(('AnophelesD_Crb','Fruitfly_CrbB'),((((('Xenopus_Crb2',('Danio_Crb1',(((('Gallus_Crb1',('Dog_Crb1',((('Chimpanzee_Crb1','Macaca_Crb1'),'HUMAN_CRUM1'),'Caw_Crb1'))),'Opossum_Crb1'),('MOUSE_CRUM1','Xenopus_Crb1')),'Takifugu_Crb1'))),'Aplysia_Crb'),(((((('Caw_Crb2',('Chimpanzee_Crb2',('Macaca_Crb2',('HUMAN_CRUM2','MOUSE_CRUM2')))),'Opossum_Crb2'),'Gallus_Crb2_iso12'),'Takifugu_Crb2'),'Danio_Crb2'),'Urchin_Crb1')),'Saccoglossus_CrbL'),'Daphnia_Crb'))),'Nasonia_Crb-iso1'),'Apis_Crb_iso1');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111391]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_5;
      LINK TAXA = TaxaForAnalysisStep22817;
      TREE 'Tree 29 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('C.elegans_CRB1',((('Nematostella_CrbB',(((O.minuta,A.vastus),'A.queenslandica_crb'),'O.lobularis_crb')),'Trichoplax_CrbB'),'Tribolium_Crb')),('Danio_Crb3',(('Xenopus_Crb3',('Trichoplax_CrbA','Nematostella_CrbA')),('C.elegans_CRB3',(('Opossum_Crb3','S.ciliatum_crb'),(('Macaca_Crb3','HUMAN_CRUM3'),'MOUSE_CRUM3')))))),(('AnophelesD_Crb','Fruitfly_CrbB'),((((('Xenopus_Crb2',('Danio_Crb1',(((('Gallus_Crb1',('Dog_Crb1',((('Chimpanzee_Crb1','Macaca_Crb1'),'HUMAN_CRUM1'),'Caw_Crb1'))),'Opossum_Crb1'),('MOUSE_CRUM1','Xenopus_Crb1')),'Takifugu_Crb1'))),'Aplysia_Crb'),(((((('Caw_Crb2',('Macaca_Crb2',('HUMAN_CRUM2',('Chimpanzee_Crb2','MOUSE_CRUM2')))),'Opossum_Crb2'),'Gallus_Crb2_iso12'),'Takifugu_Crb2'),'Danio_Crb2'),'Urchin_Crb1')),'Saccoglossus_CrbL'),'Daphnia_Crb'))),'Nasonia_Crb-iso1'),'Apis_Crb_iso1');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111400]


END;