#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 June 13, 2026; 17:29 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 22824 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep22824;
        DIMENSIONS NTAX=9;
        TAXLABELS
            'A.digitifera/340-433'
            'D.melanogaster_Bazooka/308-398'
            'M.leidyi_PAR3/272-361'
            'M.musculus_PAR3/269-363'
            'O.lobularis_PAR3_G/182-275'
            'O.minuta_PAR3/424-512'
            'P.ficiformis_PAR3/760-854'
            'S.ciliatum_PAR3/489-583'
            'T.adhaerens_PAR3/221-237'
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M45609]

	TITLE 'Character Matrix figure S2-PDZ1';
	LINK TAXA = TaxaForAnalysisStep22824;
	DIMENSIONS NCHAR=99;
	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         ]
[                                           .         .         .         .         .         .         .         .         .         ]
'A.digitifera/340-433'             EPDMLTIELKRDNSIEGLGFTVAGYRTADGRELGLIVRDISPSGCAA-RDGRLEIADRIVEVNGWSLMDIPNERAEEIFAAAIKS-PTVSLGISRS---
'D.melanogaster_Bazooka/308-398'   KDGEMLLIINEYGSP--LGLTALPDKEHGG---GLLVQHVEPGSRAE--RGQLRRDDRILEINGIKLIGLTESQVQEQLRRALES-SELRVRVLRGDRN
'M.leidyi_PAR3/272-361'            APETLKIEIVRDNLP--LGCVV---RHMDGRLPGLYIMSVDAGSAAE-RDGTLKLGDKILEVNGVDLSVMPSVSVVDVYNEMTST-AQVRLTVQRLP--
'M.musculus_PAR3/269-363'          DDMVKLVQVPNDGGP--LGIHVVPFSARGGRTLGLLVKRLEKGGKAE-QENLFHENDCIVRINDGDLRNRRFEQAQHMFRQAMRA-RVIWFHVVPAANK
'O.lobularis_PAR3_G/182-275'       GDDVRVVDIKKLGDM--LGIRAHGYKSSGGKDMGIFVQEIDKAKCKTLGDEPLLVTDRIVKINGKPVGDLSNKEALEVLAETSRNFIQIQLGVVRT---
'O.minuta_PAR3/424-512'            IPKDHNLSLPRTDSP--LSISLATNKNNSN---APVDTRNEYTNTLD-NNTLVQEDPSNVEVRTLPLVTPPIQQPEHHIDKVIES--AIELPEERPI--
'P.ficiformis_PAR3/760-854'        EHKLHIVELLRGTEP--LGITLVSY-TSQGKDLGVFISEMDSEGFAA-TSGKLQVSDRILACNGEDFCKESNKRVEERFLDMATNEPLLRMAISRGLLL
'S.ciliatum_PAR3/489-583'          GQEVADIELSCRSSKDEAGVFVRGYRTSDDRDIGVFVHDILPGSVAA-ENGLIRIADRLICVNGIDLTELSNNQAVALFQDAVRK-GNMKLQVSRAL--
'T.adhaerens_PAR3/221-237'         --------------------------TSDDENKGKILDKIGKT--------------------------------------------------------
;
END;

[ The following blocks are output data for analysis step 22824 ]
BEGIN TREES;
      TITLE 'heuristic tree alignment fig S2-PDZ1';
      LINK TAXA = TaxaForAnalysisStep22824;
      TREE 'Tree 14 from search (criterion: minimize Tree value using character matrix)' = [&R] (('M.musculus_PAR3/269-363',((('O.minuta_PAR3/424-512','T.adhaerens_PAR3/221-237'),(('M.leidyi_PAR3/272-361','S.ciliatum_PAR3/489-583'),'A.digitifera/340-433')),('P.ficiformis_PAR3/760-854','O.lobularis_PAR3_G/182-275'))),'D.melanogaster_Bazooka/308-398');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111277]


END;
BEGIN TREES;
      TITLE 'heuristic tree alignment fig S2-PDZ1';
      LINK TAXA = TaxaForAnalysisStep22824;
      TREE 'Tree 11 from search (criterion: minimize Tree value using character matrix)' = [&R] ('T.adhaerens_PAR3/221-237',('O.minuta_PAR3/424-512',((('D.melanogaster_Bazooka/308-398','M.musculus_PAR3/269-363'),('P.ficiformis_PAR3/760-854','O.lobularis_PAR3_G/182-275')),(('M.leidyi_PAR3/272-361','S.ciliatum_PAR3/489-583'),'A.digitifera/340-433'))));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111274]


END;
BEGIN TREES;
      TITLE 'heuristic tree alignment fig S2-PDZ1';
      LINK TAXA = TaxaForAnalysisStep22824;
      TREE 'Tree 1 from search (criterion: minimize Tree value using character matrix)' = [&R] ('S.ciliatum_PAR3/489-583',('M.leidyi_PAR3/272-361',(((('D.melanogaster_Bazooka/308-398','M.musculus_PAR3/269-363'),('P.ficiformis_PAR3/760-854','O.lobularis_PAR3_G/182-275')),('O.minuta_PAR3/424-512','T.adhaerens_PAR3/221-237')),'A.digitifera/340-433')));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111264]


END;
BEGIN TREES;
      TITLE 'heuristic tree alignment fig S2-PDZ1';
      LINK TAXA = TaxaForAnalysisStep22824;
      TREE 'Tree 8 from search (criterion: minimize Tree value using character matrix)' = [&R] ((('D.melanogaster_Bazooka/308-398','M.musculus_PAR3/269-363'),(('O.minuta_PAR3/424-512','T.adhaerens_PAR3/221-237'),(('M.leidyi_PAR3/272-361','S.ciliatum_PAR3/489-583'),'A.digitifera/340-433'))),('P.ficiformis_PAR3/760-854','O.lobularis_PAR3_G/182-275'));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111271]


END;
BEGIN TREES;
      TITLE 'heuristic tree alignment fig S2-PDZ1';
      LINK TAXA = TaxaForAnalysisStep22824;
      TREE 'Tree 12 from search (criterion: minimize Tree value using character matrix)' = [&R] (('P.ficiformis_PAR3/760-854',(('D.melanogaster_Bazooka/308-398','M.musculus_PAR3/269-363'),(('O.minuta_PAR3/424-512','T.adhaerens_PAR3/221-237'),(('M.leidyi_PAR3/272-361','S.ciliatum_PAR3/489-583'),'A.digitifera/340-433')))),'O.lobularis_PAR3_G/182-275');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111275]


END;
BEGIN TREES;
      TITLE 'heuristic tree alignment fig S2-PDZ1';
      LINK TAXA = TaxaForAnalysisStep22824;
      TREE 'Tree 3 from search (criterion: minimize Tree value using character matrix)' = [&R] ('M.leidyi_PAR3/272-361',('S.ciliatum_PAR3/489-583',(((('D.melanogaster_Bazooka/308-398','M.musculus_PAR3/269-363'),('P.ficiformis_PAR3/760-854','O.lobularis_PAR3_G/182-275')),('O.minuta_PAR3/424-512','T.adhaerens_PAR3/221-237')),'A.digitifera/340-433')));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111266]


END;
BEGIN TREES;
      TITLE 'heuristic tree alignment fig S2-PDZ1';
      LINK TAXA = TaxaForAnalysisStep22824;
      TREE 'Tree 15 from search (criterion: minimize Tree value using character matrix)' = [&R] ('M.musculus_PAR3/269-363',('D.melanogaster_Bazooka/308-398',((('O.minuta_PAR3/424-512','T.adhaerens_PAR3/221-237'),(('M.leidyi_PAR3/272-361','S.ciliatum_PAR3/489-583'),'A.digitifera/340-433')),('P.ficiformis_PAR3/760-854','O.lobularis_PAR3_G/182-275'))));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111278]


END;
BEGIN TREES;
      TITLE 'heuristic tree alignment fig S2-PDZ1';
      LINK TAXA = TaxaForAnalysisStep22824;
      TREE 'Tree 10 from search (criterion: minimize Tree value using character matrix)' = [&R] (('T.adhaerens_PAR3/221-237',((('D.melanogaster_Bazooka/308-398','M.musculus_PAR3/269-363'),('P.ficiformis_PAR3/760-854','O.lobularis_PAR3_G/182-275')),(('M.leidyi_PAR3/272-361','S.ciliatum_PAR3/489-583'),'A.digitifera/340-433'))),'O.minuta_PAR3/424-512');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111273]


END;
BEGIN TREES;
      TITLE 'heuristic tree alignment fig S2-PDZ1';
      LINK TAXA = TaxaForAnalysisStep22824;
      TREE 'Tree 9 from search (criterion: minimize Tree value using character matrix)' = [&R] (('D.melanogaster_Bazooka/308-398','M.musculus_PAR3/269-363'),((('O.minuta_PAR3/424-512','T.adhaerens_PAR3/221-237'),(('M.leidyi_PAR3/272-361','S.ciliatum_PAR3/489-583'),'A.digitifera/340-433')),('P.ficiformis_PAR3/760-854','O.lobularis_PAR3_G/182-275')));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111272]


END;
BEGIN TREES;
      TITLE 'heuristic tree alignment fig S2-PDZ1';
      LINK TAXA = TaxaForAnalysisStep22824;
      TREE 'Tree 4 from search (criterion: minimize Tree value using character matrix)' = [&R] ((((('D.melanogaster_Bazooka/308-398','M.musculus_PAR3/269-363'),('P.ficiformis_PAR3/760-854','O.lobularis_PAR3_G/182-275')),('O.minuta_PAR3/424-512','T.adhaerens_PAR3/221-237')),('M.leidyi_PAR3/272-361','S.ciliatum_PAR3/489-583')),'A.digitifera/340-433');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111267]


END;
BEGIN TREES;
      TITLE 'heuristic tree alignment fig S2-PDZ1';
      LINK TAXA = TaxaForAnalysisStep22824;
      TREE 'Tree 5 from search (criterion: minimize Tree value using character matrix)' = [&R] (((('D.melanogaster_Bazooka/308-398','M.musculus_PAR3/269-363'),('P.ficiformis_PAR3/760-854','O.lobularis_PAR3_G/182-275')),('O.minuta_PAR3/424-512','T.adhaerens_PAR3/221-237')),(('M.leidyi_PAR3/272-361','S.ciliatum_PAR3/489-583'),'A.digitifera/340-433'));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111268]


END;
BEGIN TREES;
      TITLE 'heuristic tree alignment fig S2-PDZ1';
      LINK TAXA = TaxaForAnalysisStep22824;
      TREE 'Tree 7 from search (criterion: minimize Tree value using character matrix)' = [&R] (('O.minuta_PAR3/424-512','T.adhaerens_PAR3/221-237'),((('D.melanogaster_Bazooka/308-398','M.musculus_PAR3/269-363'),('P.ficiformis_PAR3/760-854','O.lobularis_PAR3_G/182-275')),(('M.leidyi_PAR3/272-361','S.ciliatum_PAR3/489-583'),'A.digitifera/340-433')));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111270]


END;
BEGIN TREES;
      TITLE 'heuristic tree alignment fig S2-PDZ1';
      LINK TAXA = TaxaForAnalysisStep22824;
      TREE 'Tree 6 from search (criterion: minimize Tree value using character matrix)' = [&R] ((('O.minuta_PAR3/424-512','T.adhaerens_PAR3/221-237'),(('M.leidyi_PAR3/272-361','S.ciliatum_PAR3/489-583'),'A.digitifera/340-433')),(('D.melanogaster_Bazooka/308-398','M.musculus_PAR3/269-363'),('P.ficiformis_PAR3/760-854','O.lobularis_PAR3_G/182-275')));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111269]


END;
BEGIN TREES;
      TITLE 'heuristic tree alignment fig S2-PDZ1';
      LINK TAXA = TaxaForAnalysisStep22824;
      TREE 'Tree 2 from search (criterion: minimize Tree value using character matrix)' = [&R] (('M.leidyi_PAR3/272-361','S.ciliatum_PAR3/489-583'),(((('D.melanogaster_Bazooka/308-398','M.musculus_PAR3/269-363'),('P.ficiformis_PAR3/760-854','O.lobularis_PAR3_G/182-275')),('O.minuta_PAR3/424-512','T.adhaerens_PAR3/221-237')),'A.digitifera/340-433'));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111265]


END;
BEGIN TREES;
      TITLE 'heuristic tree alignment fig S2-PDZ1';
      LINK TAXA = TaxaForAnalysisStep22824;
      TREE 'Tree 13 from search (criterion: minimize Tree value using character matrix)' = [&R] ('P.ficiformis_PAR3/760-854',((('D.melanogaster_Bazooka/308-398','M.musculus_PAR3/269-363'),(('O.minuta_PAR3/424-512','T.adhaerens_PAR3/221-237'),(('M.leidyi_PAR3/272-361','S.ciliatum_PAR3/489-583'),'A.digitifera/340-433'))),'O.lobularis_PAR3_G/182-275'));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr111276]


END;