#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; 9:13 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 22814 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep22814;
        DIMENSIONS NTAX=17;
        TAXLABELS
            Amphimedon_queenslandica
            Aphrocalites_vastus
            Bos_floridae
            Ciona_intestinalis
            Drosophila_melanogaster
            Gallus_gallus
            Leucosolenia_complicata
            Mnemiopsis_leidyi
            Mus_musculus
            Nematostella_vectensis
            Oopsacas_minuta
            Oscarella_lobularis
            'Oscarella sp.SN-2011'
            Petrosia_ficiformis
            Sycon_ciliatum
            Sycon_coactum
            Trichoplax_adhaerens
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M45572]

	TITLE Character_Matrix_figure_1C_tree;
	LINK TAXA = TaxaForAnalysisStep22814;
	DIMENSIONS NCHAR=70;
	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]
[                                     .         .         .         .         .         .         .]
Amphimedon_queenslandica     ANN---TVQ--DIDSLREYSD-EGI--EINDGGSLSDI-SQVSFE-----LYTFQQLREAGDPFTNVAD-
Aphrocalites_vastus          VMLRREAFLC-DDDSNRHFSDSEG---DEILTNSLSRDSELNSLH-----MVSIGTIYELGSPFKQLHDV
Bos_floridae                 ADND-PTAP--PHDSIQPYDY-EG---QGSTAGSLSSLTSASSED-----DQDYEYLDNWGPQFRNLADM
Ciona_intestinalis           ADND-PTAP--PFDSLLVFDY-EG---QGSDAGSLSSLNSGTTDA-----SQDYDYLNNWGPRFKKLADM
Drosophila_melanogaster      CDRD-VGAT--TVDDVRHYAY-EG---DGNSDGSLSSLASCTDDG-----DLNFDYLSNFGPRFRKLADM
Gallus_gallus                ADTD-PTAP--PYDSLLVFDY-EG---GGSEATSLSSLNSSASDQ-----DQDYDYLNEWGNRFKKLAEL
Leucosolenia_complicata      SGLQSAHIG--AEDQATRYRV-EDEHRADYDDEQLSIDEDCSAQNQ----PADMPDPRTLGGAFANISSL
Mnemiopsis_leidyi            VD---------EPNALECQRR-DK---DSGLAGSLNTLCHFDMDC------NNENYLQDWGPKVQNLVHV
Mus_musculus                 ADSD-PTAP--PYDSLLVFDY-EG---SGSEAASLSSLNSSESDQ-----DQDYDYLNEWGNRFKKLADM
Nematostella_vectensis       TDRE--VFL--AVDELHIYRY-EG---DDTDVDDLSEIEPDEEDEEY---EQEFDFLKQWGPKFDKLAKL
Oopsacas_minuta              VILRREAYLC-DDDSKRRYSDSEG---EETLTVSFSRDSEFN-IS-----EVPVETLNELGSPFRKLCKV
Oscarella_lobularis          ADNLTRDAF--PSDELVCYSY-EG---CGSFAGSLSSISSSVSIT-------------------------
'Oscarella sp.SN-2011'       ADRRTEDWF--PPDELVSYIY-EG---CGSSAGSLSTVFSKQSIR-------------------------
Petrosia_ficiformis          ANK---GIY--DLDSLKGYSD-EG----VSSTGSLSTICTNTGYE-----PYTI----------------
Sycon_ciliatum               STQESTPV---SSDRAYHYAT-ESE--VDTHDGRLEEDLCPSPPS------RHIADPRSLGNDFANISQL
Sycon_coactum                NTRHQAAVMAEGTDRPHHYDT-ELE--PEHYAERLGEDLCPGESG-----PRHIDDPRSMGQDFAHISQF
Trichoplax_adhaerens         -------------DSVKYYAD-EG---KSTPAGSLSSLEVIEDDEVMEDDQASFSYLNVWGPRFKHLADI
;
END;

[ The following blocks are output data for analysis step 22814 ]
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_1C;
      LINK TAXA = TaxaForAnalysisStep22814;
      TREE 'Tree 29 from search (criterion: maximimize Tree value using character)' = [&R] ((((Trichoplax_adhaerens,Nematostella_vectensis),Drosophila_melanogaster),Bos_floridae),(((((((((((Mus_musculus,Aphrocalites_vastus),Gallus_gallus),Oopsacas_minuta),Leucosolenia_complicata),Sycon_coactum),Sycon_ciliatum),Petrosia_ficiformis),Amphimedon_queenslandica),'Oscarella sp.SN-2011'),Oscarella_lobularis),(Mnemiopsis_leidyi,Ciona_intestinalis)));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr110951]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_1C;
      LINK TAXA = TaxaForAnalysisStep22814;
      TREE 'Tree 7 from search (criterion: maximimize Tree value using character)' = [&R] (Bos_floridae,(Mnemiopsis_leidyi,((((((((((((((Mus_musculus,Aphrocalites_vastus),Gallus_gallus),Oopsacas_minuta),Leucosolenia_complicata),Sycon_coactum),Sycon_ciliatum),Petrosia_ficiformis),Amphimedon_queenslandica),'Oscarella sp.SN-2011'),Oscarella_lobularis),Trichoplax_adhaerens),Nematostella_vectensis),Drosophila_melanogaster),Ciona_intestinalis)));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr110929]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_1C;
      LINK TAXA = TaxaForAnalysisStep22814;
      TREE 'Tree 11 from search (criterion: maximimize Tree value using character)' = [&R] ((Drosophila_melanogaster,Bos_floridae),(((((((((((((Mus_musculus,Aphrocalites_vastus),Gallus_gallus),Oopsacas_minuta),Leucosolenia_complicata),Sycon_coactum),Sycon_ciliatum),Petrosia_ficiformis),Amphimedon_queenslandica),'Oscarella sp.SN-2011'),Oscarella_lobularis),Trichoplax_adhaerens),Nematostella_vectensis),(Mnemiopsis_leidyi,Ciona_intestinalis)));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr110933]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_1C;
      LINK TAXA = TaxaForAnalysisStep22814;
      TREE 'Tree 9 from search (criterion: maximimize Tree value using character)' = [&R] (((Drosophila_melanogaster,Bos_floridae),((((((((((((Mus_musculus,Aphrocalites_vastus),Gallus_gallus),Oopsacas_minuta),Leucosolenia_complicata),Sycon_coactum),Sycon_ciliatum),Petrosia_ficiformis),Amphimedon_queenslandica),'Oscarella sp.SN-2011'),Oscarella_lobularis),Trichoplax_adhaerens),Nematostella_vectensis)),(Mnemiopsis_leidyi,Ciona_intestinalis));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr110931]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_1C;
      LINK TAXA = TaxaForAnalysisStep22814;
      TREE 'Tree 18 from search (criterion: maximimize Tree value using character)' = [&R] (((Nematostella_vectensis,Drosophila_melanogaster),((((((((((((Mus_musculus,Aphrocalites_vastus),Gallus_gallus),Oopsacas_minuta),Leucosolenia_complicata),Sycon_coactum),Sycon_ciliatum),Petrosia_ficiformis),Amphimedon_queenslandica),'Oscarella sp.SN-2011'),Oscarella_lobularis),Trichoplax_adhaerens),Bos_floridae)),(Mnemiopsis_leidyi,Ciona_intestinalis));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr110940]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_1C;
      LINK TAXA = TaxaForAnalysisStep22814;
      TREE 'Tree 13 from search (criterion: maximimize Tree value using character)' = [&R] ((Drosophila_melanogaster,Bos_floridae),(Mnemiopsis_leidyi,(((((((((((((Mus_musculus,Aphrocalites_vastus),Gallus_gallus),Oopsacas_minuta),Leucosolenia_complicata),Sycon_coactum),Sycon_ciliatum),Petrosia_ficiformis),Amphimedon_queenslandica),'Oscarella sp.SN-2011'),Oscarella_lobularis),Trichoplax_adhaerens),Nematostella_vectensis),Ciona_intestinalis)));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr110935]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_1C;
      LINK TAXA = TaxaForAnalysisStep22814;
      TREE 'Tree 23 from search (criterion: maximimize Tree value using character)' = [&R] (((((Trichoplax_adhaerens,Nematostella_vectensis),Drosophila_melanogaster),Bos_floridae),((((((((((Mus_musculus,Aphrocalites_vastus),Gallus_gallus),Oopsacas_minuta),Leucosolenia_complicata),Sycon_coactum),Sycon_ciliatum),Petrosia_ficiformis),Amphimedon_queenslandica),'Oscarella sp.SN-2011'),Oscarella_lobularis)),(Mnemiopsis_leidyi,Ciona_intestinalis));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr110945]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_1C;
      LINK TAXA = TaxaForAnalysisStep22814;
      TREE 'Tree 19 from search (criterion: maximimize Tree value using character)' = [&R] (((Nematostella_vectensis,Drosophila_melanogaster),Bos_floridae),((((((((((((Mus_musculus,Aphrocalites_vastus),Gallus_gallus),Oopsacas_minuta),Leucosolenia_complicata),Sycon_coactum),Sycon_ciliatum),Petrosia_ficiformis),Amphimedon_queenslandica),'Oscarella sp.SN-2011'),Oscarella_lobularis),Trichoplax_adhaerens),(Mnemiopsis_leidyi,Ciona_intestinalis)));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr110941]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_1C;
      LINK TAXA = TaxaForAnalysisStep22814;
      TREE 'Tree 25 from search (criterion: maximimize Tree value using character)' = [&R] (((((Trichoplax_adhaerens,Nematostella_vectensis),((((((((((Mus_musculus,Aphrocalites_vastus),Gallus_gallus),Oopsacas_minuta),Leucosolenia_complicata),Sycon_coactum),Sycon_ciliatum),Petrosia_ficiformis),Amphimedon_queenslandica),'Oscarella sp.SN-2011'),Oscarella_lobularis)),Drosophila_melanogaster),Bos_floridae),(Mnemiopsis_leidyi,Ciona_intestinalis));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr110947]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_1C;
      LINK TAXA = TaxaForAnalysisStep22814;
      TREE 'Tree 6 from search (criterion: maximimize Tree value using character)' = [&R] (Bos_floridae,((Mnemiopsis_leidyi,(((((((((((((Mus_musculus,Aphrocalites_vastus),Gallus_gallus),Oopsacas_minuta),Leucosolenia_complicata),Sycon_coactum),Sycon_ciliatum),Petrosia_ficiformis),Amphimedon_queenslandica),'Oscarella sp.SN-2011'),Oscarella_lobularis),Trichoplax_adhaerens),Nematostella_vectensis),Drosophila_melanogaster)),Ciona_intestinalis));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr110928]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_1C;
      LINK TAXA = TaxaForAnalysisStep22814;
      TREE 'Tree 24 from search (criterion: maximimize Tree value using character)' = [&R] (((((Trichoplax_adhaerens,Nematostella_vectensis),Drosophila_melanogaster),((((((((((Mus_musculus,Aphrocalites_vastus),Gallus_gallus),Oopsacas_minuta),Leucosolenia_complicata),Sycon_coactum),Sycon_ciliatum),Petrosia_ficiformis),Amphimedon_queenslandica),'Oscarella sp.SN-2011'),Oscarella_lobularis)),Bos_floridae),(Mnemiopsis_leidyi,Ciona_intestinalis));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr110946]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_1C;
      LINK TAXA = TaxaForAnalysisStep22814;
      TREE 'Tree 1 from search (criterion: maximimize Tree value using character)' = [&R] (((((((((((((((Mus_musculus,Aphrocalites_vastus),Gallus_gallus),Oopsacas_minuta),Leucosolenia_complicata),Sycon_coactum),Sycon_ciliatum),Petrosia_ficiformis),Amphimedon_queenslandica),'Oscarella sp.SN-2011'),Oscarella_lobularis),Trichoplax_adhaerens),Nematostella_vectensis),Drosophila_melanogaster),Bos_floridae),(Mnemiopsis_leidyi,Ciona_intestinalis));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr110923]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_1C;
      LINK TAXA = TaxaForAnalysisStep22814;
      TREE 'Tree 17 from search (criterion: maximimize Tree value using character)' = [&R] (((Nematostella_vectensis,((((((((((((Mus_musculus,Aphrocalites_vastus),Gallus_gallus),Oopsacas_minuta),Leucosolenia_complicata),Sycon_coactum),Sycon_ciliatum),Petrosia_ficiformis),Amphimedon_queenslandica),'Oscarella sp.SN-2011'),Oscarella_lobularis),Trichoplax_adhaerens),Drosophila_melanogaster)),Bos_floridae),(Mnemiopsis_leidyi,Ciona_intestinalis));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr110939]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_1C;
      LINK TAXA = TaxaForAnalysisStep22814;
      TREE 'Tree 28 from search (criterion: maximimize Tree value using character)' = [&R] ((((Trichoplax_adhaerens,Nematostella_vectensis),Drosophila_melanogaster),(((((((((((Mus_musculus,Aphrocalites_vastus),Gallus_gallus),Oopsacas_minuta),Leucosolenia_complicata),Sycon_coactum),Sycon_ciliatum),Petrosia_ficiformis),Amphimedon_queenslandica),'Oscarella sp.SN-2011'),Oscarella_lobularis),Bos_floridae)),(Mnemiopsis_leidyi,Ciona_intestinalis));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr110950]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_1C;
      LINK TAXA = TaxaForAnalysisStep22814;
      TREE 'Tree 14 from search (criterion: maximimize Tree value using character)' = [&R] ((((Nematostella_vectensis,Drosophila_melanogaster),Bos_floridae),(Mnemiopsis_leidyi,Ciona_intestinalis)),(((((((((((Mus_musculus,Aphrocalites_vastus),Gallus_gallus),Oopsacas_minuta),Leucosolenia_complicata),Sycon_coactum),Sycon_ciliatum),Petrosia_ficiformis),Amphimedon_queenslandica),'Oscarella sp.SN-2011'),Oscarella_lobularis),Trichoplax_adhaerens));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr110936]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_1C;
      LINK TAXA = TaxaForAnalysisStep22814;
      TREE 'Tree 21 from search (criterion: maximimize Tree value using character)' = [&R] (((Nematostella_vectensis,Drosophila_melanogaster),Bos_floridae),(Mnemiopsis_leidyi,((((((((((((Mus_musculus,Aphrocalites_vastus),Gallus_gallus),Oopsacas_minuta),Leucosolenia_complicata),Sycon_coactum),Sycon_ciliatum),Petrosia_ficiformis),Amphimedon_queenslandica),'Oscarella sp.SN-2011'),Oscarella_lobularis),Trichoplax_adhaerens),Ciona_intestinalis)));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr110943]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_1C;
      LINK TAXA = TaxaForAnalysisStep22814;
      TREE 'Tree 8 from search (criterion: maximimize Tree value using character)' = [&R] (((Drosophila_melanogaster,Bos_floridae),(Mnemiopsis_leidyi,Ciona_intestinalis)),((((((((((((Mus_musculus,Aphrocalites_vastus),Gallus_gallus),Oopsacas_minuta),Leucosolenia_complicata),Sycon_coactum),Sycon_ciliatum),Petrosia_ficiformis),Amphimedon_queenslandica),'Oscarella sp.SN-2011'),Oscarella_lobularis),Trichoplax_adhaerens),Nematostella_vectensis));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr110930]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_1C;
      LINK TAXA = TaxaForAnalysisStep22814;
      TREE 'Tree 2 from search (criterion: maximimize Tree value using character)' = [&R] ((Mnemiopsis_leidyi,((((((((((((((Mus_musculus,Aphrocalites_vastus),Gallus_gallus),Oopsacas_minuta),Leucosolenia_complicata),Sycon_coactum),Sycon_ciliatum),Petrosia_ficiformis),Amphimedon_queenslandica),'Oscarella sp.SN-2011'),Oscarella_lobularis),Trichoplax_adhaerens),Nematostella_vectensis),Drosophila_melanogaster),Bos_floridae)),Ciona_intestinalis);
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr110924]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_1C;
      LINK TAXA = TaxaForAnalysisStep22814;
      TREE 'Tree 20 from search (criterion: maximimize Tree value using character)' = [&R] (((Nematostella_vectensis,Drosophila_melanogaster),Bos_floridae),((Mnemiopsis_leidyi,(((((((((((Mus_musculus,Aphrocalites_vastus),Gallus_gallus),Oopsacas_minuta),Leucosolenia_complicata),Sycon_coactum),Sycon_ciliatum),Petrosia_ficiformis),Amphimedon_queenslandica),'Oscarella sp.SN-2011'),Oscarella_lobularis),Trichoplax_adhaerens)),Ciona_intestinalis));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr110942]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_1C;
      LINK TAXA = TaxaForAnalysisStep22814;
      TREE 'Tree 10 from search (criterion: maximimize Tree value using character)' = [&R] ((Drosophila_melanogaster,(((((((((((((Mus_musculus,Aphrocalites_vastus),Gallus_gallus),Oopsacas_minuta),Leucosolenia_complicata),Sycon_coactum),Sycon_ciliatum),Petrosia_ficiformis),Amphimedon_queenslandica),'Oscarella sp.SN-2011'),Oscarella_lobularis),Trichoplax_adhaerens),Nematostella_vectensis),Bos_floridae)),(Mnemiopsis_leidyi,Ciona_intestinalis));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr110932]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_1C;
      LINK TAXA = TaxaForAnalysisStep22814;
      TREE 'Tree 26 from search (criterion: maximimize Tree value using character)' = [&R] ((((Trichoplax_adhaerens,(((((((((((Mus_musculus,Aphrocalites_vastus),Gallus_gallus),Oopsacas_minuta),Leucosolenia_complicata),Sycon_coactum),Sycon_ciliatum),Petrosia_ficiformis),Amphimedon_queenslandica),'Oscarella sp.SN-2011'),Oscarella_lobularis),Nematostella_vectensis)),Drosophila_melanogaster),Bos_floridae),(Mnemiopsis_leidyi,Ciona_intestinalis));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr110948]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_1C;
      LINK TAXA = TaxaForAnalysisStep22814;
      TREE 'Tree 5 from search (criterion: maximimize Tree value using character)' = [&R] (Bos_floridae,((((((((((((((Mus_musculus,Aphrocalites_vastus),Gallus_gallus),Oopsacas_minuta),Leucosolenia_complicata),Sycon_coactum),Sycon_ciliatum),Petrosia_ficiformis),Amphimedon_queenslandica),'Oscarella sp.SN-2011'),Oscarella_lobularis),Trichoplax_adhaerens),Nematostella_vectensis),Drosophila_melanogaster),(Mnemiopsis_leidyi,Ciona_intestinalis)));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr110927]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_1C;
      LINK TAXA = TaxaForAnalysisStep22814;
      TREE 'Tree 15 from search (criterion: maximimize Tree value using character)' = [&R] ((((Nematostella_vectensis,Drosophila_melanogaster),Bos_floridae),(((((((((((Mus_musculus,Aphrocalites_vastus),Gallus_gallus),Oopsacas_minuta),Leucosolenia_complicata),Sycon_coactum),Sycon_ciliatum),Petrosia_ficiformis),Amphimedon_queenslandica),'Oscarella sp.SN-2011'),Oscarella_lobularis),Trichoplax_adhaerens)),(Mnemiopsis_leidyi,Ciona_intestinalis));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr110937]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_1C;
      LINK TAXA = TaxaForAnalysisStep22814;
      TREE 'Tree 4 from search (criterion: maximimize Tree value using character)' = [&R] ((Bos_floridae,(Mnemiopsis_leidyi,Ciona_intestinalis)),(((((((((((((Mus_musculus,Aphrocalites_vastus),Gallus_gallus),Oopsacas_minuta),Leucosolenia_complicata),Sycon_coactum),Sycon_ciliatum),Petrosia_ficiformis),Amphimedon_queenslandica),'Oscarella sp.SN-2011'),Oscarella_lobularis),Trichoplax_adhaerens),Nematostella_vectensis),Drosophila_melanogaster));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr110926]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_1C;
      LINK TAXA = TaxaForAnalysisStep22814;
      TREE 'Tree 3 from search (criterion: maximimize Tree value using character)' = [&R] (Mnemiopsis_leidyi,(((((((((((((((Mus_musculus,Aphrocalites_vastus),Gallus_gallus),Oopsacas_minuta),Leucosolenia_complicata),Sycon_coactum),Sycon_ciliatum),Petrosia_ficiformis),Amphimedon_queenslandica),'Oscarella sp.SN-2011'),Oscarella_lobularis),Trichoplax_adhaerens),Nematostella_vectensis),Drosophila_melanogaster),Bos_floridae),Ciona_intestinalis));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr110925]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_1C;
      LINK TAXA = TaxaForAnalysisStep22814;
      TREE 'Tree 22 from search (criterion: maximimize Tree value using character)' = [&R] (((((Trichoplax_adhaerens,Nematostella_vectensis),Drosophila_melanogaster),Bos_floridae),(Mnemiopsis_leidyi,Ciona_intestinalis)),((((((((((Mus_musculus,Aphrocalites_vastus),Gallus_gallus),Oopsacas_minuta),Leucosolenia_complicata),Sycon_coactum),Sycon_ciliatum),Petrosia_ficiformis),Amphimedon_queenslandica),'Oscarella sp.SN-2011'),Oscarella_lobularis));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr110944]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_1C;
      LINK TAXA = TaxaForAnalysisStep22814;
      TREE 'Tree 1 from search (criterion: maximimize Tree value using character)' = [&R] (((((((((((((((Mus_musculus,Aphrocalites_vastus),Gallus_gallus),Oopsacas_minuta),Leucosolenia_complicata),Sycon_coactum),Sycon_ciliatum),Petrosia_ficiformis),Amphimedon_queenslandica),'Oscarella sp.SN-2011'),Oscarella_lobularis),Trichoplax_adhaerens),Nematostella_vectensis),Drosophila_melanogaster),Bos_floridae),(Mnemiopsis_leidyi,Ciona_intestinalis));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr110952]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_1C;
      LINK TAXA = TaxaForAnalysisStep22814;
      TREE 'Tree 27 from search (criterion: maximimize Tree value using character)' = [&R] ((((Trichoplax_adhaerens,Nematostella_vectensis),(((((((((((Mus_musculus,Aphrocalites_vastus),Gallus_gallus),Oopsacas_minuta),Leucosolenia_complicata),Sycon_coactum),Sycon_ciliatum),Petrosia_ficiformis),Amphimedon_queenslandica),'Oscarella sp.SN-2011'),Oscarella_lobularis),Drosophila_melanogaster)),Bos_floridae),(Mnemiopsis_leidyi,Ciona_intestinalis));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr110949]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_1C;
      LINK TAXA = TaxaForAnalysisStep22814;
      TREE 'Tree 12 from search (criterion: maximimize Tree value using character)' = [&R] ((Drosophila_melanogaster,Bos_floridae),((Mnemiopsis_leidyi,((((((((((((Mus_musculus,Aphrocalites_vastus),Gallus_gallus),Oopsacas_minuta),Leucosolenia_complicata),Sycon_coactum),Sycon_ciliatum),Petrosia_ficiformis),Amphimedon_queenslandica),'Oscarella sp.SN-2011'),Oscarella_lobularis),Trichoplax_adhaerens),Nematostella_vectensis)),Ciona_intestinalis));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr110934]


END;
BEGIN TREES;
      TITLE heuristic_tree_alignment_fig_1C;
      LINK TAXA = TaxaForAnalysisStep22814;
      TREE 'Tree 16 from search (criterion: maximimize Tree value using character)' = [&R] ((((Nematostella_vectensis,Drosophila_melanogaster),(((((((((((Mus_musculus,Aphrocalites_vastus),Gallus_gallus),Oopsacas_minuta),Leucosolenia_complicata),Sycon_coactum),Sycon_ciliatum),Petrosia_ficiformis),Amphimedon_queenslandica),'Oscarella sp.SN-2011'),Oscarella_lobularis),Trichoplax_adhaerens)),Bos_floridae),(Mnemiopsis_leidyi,Ciona_intestinalis));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr110938]


END;