#NEXUS

BEGIN TAXA;
	TITLE Taxa;
	DIMENSIONS NTAX=28;
	TAXLABELS
		Cyanidioschyzon_merolae Galdieria_sulphuralia Porphyra_yezoensis Porphyridium_purpureum Neorhodella_cyanea Dixoniella_grisea Guillardia_theta Pyrenomonas_helgolandii Cryptomonas_ovata Chroomonas_caudata Aureococcus_anophagefferens Heterosigma_akashiwo Vaucheria_litorea Vaucheria_frigida Botrydium_granulatum Fucus_distichus Phaeodactylum_tricornutum Chaetoceros_gracilis Thalassiosira_pseudonana Kryptoperidinium_foliaceum Karlodinium_veneficum Pavlova_lutheri Karenia_brevis Isochrysis_galbana Emiliania_huxleii Prymnesium_parvum Heterocapsa_triquetra Amphidinium_carterae 
	;

END;


BEGIN CHARACTERS;
	TITLE  Dinophyta_pbsO;
	DIMENSIONS  NCHAR=219;
	FORMAT DATATYPE = Protein GAP = - MISSING = X;
	MATRIX
	Cyanidioschyzon_merolae      VQA--LTAQDVRQLSYEQVKGTGLANRCPEVVKVVDLCLEPKQFLVEEEFVDTKLMTRATYTLANIEGELVWKFIEKDGMDYAATTVQIPGGERVPFLFSIKKLVASLISTSTELGGEFKVPSYRTGMFLDPKGRGMANGYDMAVALPALEAVGQEVLRKENDKVFQETSGRIELAVNKVDPTSNEIGGVFVSEQLSDTDMGAKEPKKLLLKGVFYARI
	Galdieria_sulphuralia        SLA--LTRSDIRSLTYDQVKGTGIASRCPEVDKLVDLCLEPKSFQVEEEFVDAKLVTRATYTLSNIEGTLNLVFRERDGLDYAACTVQLPGGERVPFLFSIKKLVAKAINTATEFGGQFKVTGYRTGLFLDPKGRGGTSGYDMAVALPAREAEGQDDLLRENNKTFDVTDGSIEMAVNKLDPTSGEIAGVFVSEQLSDTDMGAKDPKKLLLKGIFYARV
	Porphyra_yezoensis           AAA--LTSADIRSLTYEQVKGTGLANRCPEVDKLVDLCLEPKSFQVEEEFVDTKLMTRATYTLSGIEGILRLVFEEKEGIDYAATTVQLPGGERLPFLFTIKQLVAKAISTATEFGGTYRVPSYRTGGFLDPKGRGMVTGYDMAVGLPAMEAEGQTKLFKETNKVFEVTDGEIEMAVNKLDAASGELGGVFVAEQLSDTDMGAKAPKNVLVKGVFYGRV
	Porphyridium_purpureum       VQA--FTEEDFRQLSYEQVKGTGLANRCPEVDKIVDMCIEPKSFQVEDEFVDTKLMTRATYTLTGIEGPLTLEFQEKDGIDYAATTVQLPGGERVPFLFTVKELVATAIGSGTEFGGEFTVPSYRTGLFLDPKGRGGVTGYDMAVALPGMMAEGQDELFKETNKVFQVTKGEIEMGVQKVDPSTNEIAGVFVSEQLTDTDMGAKAPKNILLKGVFYARI
	Neorhodella_cyanea           AQA--LTTSDIRGLSYDQVKGTGLANRCPEVDKTVDMCIEPKSFQVEEEYVDTKLMTRATYTLTGIEGPLTLTFVEKDGIDYAATTVQLPGGERVPFLFTVKELVAKGISTATEFGGDFRVPSYRTGLFLDPKGRGGVTGYDMAVALPGKEAEGQDDIFKETNKVFQITDGSIEMAVNKIDVETKEFAGVFVSEQLSDTDMGAKTPKKVLLKGVFYGRL
	Dixoniella_grisea            AQA--LTSADIRGLSYEQIKGTGLANRCPEVDKIVDMCIEPKSFQVEEEYVDTKLMTRATYTLTGITGPLELTFTEVDGIDYAATTVQLPGGERVPFLFTVKELVAKAISTATEFGGDFKVPSYRAGTFLDPKGRGMTTGYDMAVALPAMEAEGQEELFKETNKVFQVTDGSIEMAVNKVDPETGEFAGVFVSEQLSDTDMGAKAPKKLLLKGVFYARV
	Guillardia_theta             ANA--LTSKDINNLTYEEVKGTGIANRCPEVEKITDLCIEPKSFQIETEFVDTKLVTRATYSLAGVEGPLFLTFQEKEGLDYAATTVQLPGGERVPFFFTIKELVAKAISPGTEFGGTFTVPSYRSGLFLDPKGRGATTGYDMAQALPAFEAEGQAELFKENNKVFQVTDGSMEFAVNKVDGQTGEFSGVFVSEQLSDTDMGSKAPKKVLIKGIVYGKV
	Pyrenomonas_helgolandii      ANA--LSSADVRSLTYQQIKGTGLANRCPEVEKITDLCLEPKSFQIEEEFVDTKLMTRATYTLAGVEGPLFLTFLEKEGIDYAATTVQLPGGERVPFMFTVKDLEAKSISAGTEFGGTFKVPSYRSGLFLDPKGRGGTTGYDMAQALPGMEAEGQEELFKETNKVFQVTDGTIEFAVNKVDAATGEFSGVFVSEQLSDTDMGSKAPKKVLLKGIIFGKV
	Cryptomonas_ovata            ADA--LTTQDIRDLTYGQIKGTGIANRCPEVAKIVDLCLEPKSFQIEEEFVDTKLMTRATYSLTGVEGPLFLTFLEKGGIDYAPATVQLPGGERVPFMFTIKQLEAKSIAPGTEFGGTFTVPSYRSGLFLDPKGRGGTTGYDNAGALVALEAEGQEELFKETNKVYQVTDGSIEFAVNKVDGASGEFSGVFVSEQLSDTDMGSKAPKKVLLKGILFGRV
	Chroomonas_caudata           ADA--LTTQDIKSLTYLQIKGTGLANRCPEVSKIVDMCLEPKSWQIEEEFVDTKLMNRATYTLTGIEGPLVLVFYEKEGIDYAPTTVQLPGGERVPFLFNVKELVASFIKAGVEFGGNFRTPSYRTGLFLDPKGRGGTTGYDMAVALPALEAEGQSELFAETNKVFQVTDGSIEMAITKVDATTGEFSGVFVSEQLSDTDMGSKAPKKVLLKGIVFAKV
	Aureococcus_anophagefferens  ANA--ITSEVRNQLSYEQVKGTGLANRCNEVVSLVDVCLEPKTWQVEEQFVNTKLMTRQTYTLDGISGKLSITFTEEDGIDYAPTTVQLPGGERVPFLFTVKELVAKGFKPGYEFGGTFKVPSYRTGLFLDPKGRGMTTGYDQAQALAASQTDSQGELEGEINKVFDVFDGTIEFAVSQVNAAEGEIGGVFVSSQASDTDLGSKTPKKVLSKGIFYGRV
	Heterosigma_akashiwo         AFA--ITKAESNSLDYLQVKGTGLANRCSEVIQLVDLCIEPKTFQVEEEFVNTKLMTRQTYTLDGISGTISIVFTEEDGIDYAASTVQKPGGERVPFLFTVKELVATAIAPGFQMGGKFTVPSYRTGLFLDPKGRGMSTGYDMAVALPGKQSEGDAELFKENNKVFDVLGGQIEFEVNRVNAEEGEIGGVFVSTQASDTDMGGKEPQTILLKGIFYGRI
	Vaucheria_litorea            VEA--ITKDQIESLSYLQVKGTGLANRCPEVFKIVDMCIEPKTFQVLEEYVNTKLMTRQTYTLYGIDGSFAITFREKDGIDYAATTIQLPGGERVPFLFTVKELVAQAVTPGLQFGGPFSTPSYRTGLFLDPKGRGGSTGYDMAVALPGKQSEGDAELFGENNKTFDVTKGNIEFEVNRVDPSNGEIGGVFVSKQKGDTDMGSKVPKDLLIKGIFYGRL
	Vaucheria_frigida            ADA--ITKDQIDSLSYMQVKGTGLANRCPEVIKLMDLCIEPKVFQVLEEYVNTKLMTRQTYTLYGIEGSFALTFREKDGIDYAATTVQLPGGERVPFLFTVKELVAKAVAPGFQFGGGFSTPSYRTGLFLDPKGRGGSTGYDMAVALPGLQSEGDKEMFKENNKTFDVTKGQIEFEVNRVDASAGEIGGVFVSNQKGDTDMGSKTPKDVLVKGIFYGRL
	Botrydium_granulatum         AEA--ITKDQIDSLSYMQVKGTGLANRCPEVVKIVDLCIEPKVFQVLEEYVNTKLMTRQTYTLYGIEGDLTLVFTEKDGIDYAATTVQLPGGERVPFLFTVKELVAKAVAPGFQFGGAFKTPSYRTGLFLDPKGRGGSTGYDMAVALPGLQSEGDKELFDENNKTFDVTDGQIEFEVNRVDAEAGEIGGVFVSKQKGDTDMGSKVPKDMLVKGIFYGRL
	Fucus_distichus              SEA--VTRDTLDALSYTQVKGTGLANRCPEVREIIDMCIEPKQFQVLSRMIDTKLMTRETYTLYGIEGNFGLTFEEKDGIDYAATTIQSN-YERIPFLFTVKDLVAKAVKPGFQMGGGFRTPSYRTGLFLDPKGRGGSTGYDMAVALPGLQSEGDAELFKENNKVFDVTDGNIEFEVNKVDKEAGEIGGVFVSKQKGDTDMGSKVPKDILVKGIFYARI
	Phaeodactylum_tricornutum    ANA--LTKSQINELSYLQVKGTGLANRCPEVVRLVDMCIEPKAWAVEEEFVNSKVMTRQTYTLDGIEGALKIVFQEQEGIDYAATTVQLPGGERVPFLFTVKDLVAKGFKPGFQMGGDFNTPSYRTGLFLDPKGRGGTTGYDMAVALPGLQSEGDDDLFKENNKTFDITTGRIEMEVNKVNAEEQEIGGVFVATQLSDTDMGSKVPKKVLTKGIFYARV
	Chaetoceros_gracilis         AQA--LTKSQINELSYLQVKGTGLANRCAEVVKLVDMCIEPKAWAVEEEFVNSKVMTRQTYTLDAIEGPITITFNEKEGIDYAATTVQLPGGERVPFLFTVKDLVAKGFKPGFQMGGDFNTPSYRTGLFLDPKGRGGTTGYDMAVALPALQLEGDAELFGENNKVFDITQGRIEMEVNKVNAEDSEIGGVFVATQLSDTDMGSKTPKKVLTKGIFYAKV
	Thalassiosira_pseudonana     AQA--ITKSELNQLSYLQVKGTGLANRCSEVIRLVDMCIEPKAWAVEEEFVNSKVMTRQTYTLEGIEGSLKIVFTEEEGIDYAPTTVQLPGGERVPFLFTVKELVATGFKPGFQMGGDFSVPSYRTGLFLDPKGRGGVTGYDMAVALPGLQSEGDAELFKENNKTFEVGNGRIEMEVNKVNAEESEIGGVFVASQSGDTDMGSKVPKKILTKGIFYAKI
	Kryptoperidinium_foliaceum   AQA--LTKSEINELTYLQVKGTGLANRCPEVVKLVDMCIEPKAWAVEEEFVNSKVVTRQTYTLDGIEGVLSIVFKEKEGIDYAATTVQLPGGERVPFLFTVKDLVAKGFKPGFQMGGDFSVPSYRTGLFLDPKGRGGTTGYDMAVALPGLQSEGDDDLFKENNKTFDVTTGRIEMEVNKVNADEQEIGGVFVATQLGDTDMGSKVPKKILTKGIFYARV
	Karlodinium_veneficum        AKAGPFTRTELNSLTYQQIKGTGLANTCPKVE-------------------KEKVTTRQTYTLTGIEGKLSLTFTEQDGIDYAATTVQRPGGERVPFLFTVKNLVAQALEPGFEWGGKFVVPSYRTGLFLDPKGRGITTGYDQAVALPALQAGGDEALYAENNKKFDVLAGNIEMKVTSVNSELGEIGGVFVQQQPSDTDLGGKTPITLQLKGSWFATV
	Pavlova_lutheri              AQA--LSKETYNSLTYDQIKGTGLANKCPDVTKFDEFCMQPTEVSILETIIPSKMMTRQTGTLAMVEGDLVVVLKEKDGIDYAASTVQTPGGERVPYLFTVKGLIAKGVKPGLKLSGDYIVPSYRTGLFLDPKGRGTTTGYDQAVALPALQAGGDDELFKENNKKFEVLSGSTELTVXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
	Karenia_brevis               ALAGPFTRDDLASLTYDQVKGSGLANTCPKVNLSD-FCLEPTSFAILEEPVPSKVTTRQTYVLDGIEGTLSLKFVETDGIDYAPTTIQLPGGERVPFLFTVKNLVATAIAPGFTMSGPFMVPSYRTGLFLDPKGRGTTTGYDQAVALPAMQAGGDEEMFKENDKKFDVGKGSIELKVTQVNTELKEIGGVFVHKQPGDTDLGSKEPKEILLKGNWFATV
	Isochrysis_galbana           ASAGPFTREDIASLTYLQIKGTGLANTCPIVQKIEEFCLEPTSFQVLEEAVDTKVTTRQTYVLTGIDGDLVLTFLEKDGIDYAATTVQLPGGERVPFLFTVKNLVAQSISPGLKMAGSFTVPSYRTGLFLDPKGRGTTTGYDQAVALPALQAGGDESLFKENDKKFDVGTGTIEMKVTAVNAELGEFGGVFVQKQPSDTDLGSKQPKEVLLKGQFFGTV
	Emiliania_huxleii            ASAGPFTRTDIASLTYQQIKGTGLANTCPVVEKIDEFCLEPTSFQVLEEAVDTKVTTRQTYVLTGMEGDLVLTFLEKDGIDYAPTTVQLPGGERVPFLFTVKNLVAQSISPGLKMSGGFNVPSYRTGLFLDPKGRGTTTGYDQAVALPALQAGGDESLFKENNKKFDVGRGSIELKVTSVNAELGEFGGVFVQKQPSDTDLGSKVPKELLLKGQFFGTV
	Prymnesium_parvum            ASAGPFTRSEIASLTYEQIKGTGLANTCPIVEKIDEFCLEPTSFQVLEEAVNTKVTTRQTYVLTGIEGDLTLKFTEKDGIDYAPTTVQLPGGERVPFLFTVKNLIATSIESGTKLAGKFTVPSYRTGLFLDPKGRGTTTGYDQAVALPALQAGGDESLFAENNKKFDVGSGSIELKVTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
	Heterocapsa_triquetra        AKA--ITAEQFSQLTYAQVRGSGLANRCPTVERMQNFCLEPKSFAIEFEFVTTKLTTRQTYTLAFIEGALKITFTEQDGMDFAATTVKMPDGEYVPFLFSCKQLIAKGFKPGFTWGGEFNVPSYRTGGFLDPKGRGMYTGYDQAVALPALQAGGQEELFKETNKVFDIGKGAIEMEVNKVNQELGEIGGVFVSKQPSDTDMGAKAPKTVLLKGIFYGKI
	Amphidinium_carterae         ARA--ITSEQFEQLTYEQVKGSGLANRCPTVERMKKMCFEPKSFAVEAEFVNTRLVTRQTYTLEQIEGQLKLTFVEEDGIDFAASTVQLPNGERVPFLFTMKKLVAKGFKPGFTWGGEYEVPSYRTGGFLDPKGRGMYSGYDQAVALPALQAXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

;


END;


BEGIN TREES;
	Title Dinophyta_pbsO_TB;
	LINK Taxa = Taxa;
	TRANSLATE
		1 Cyanidioschyzon_merolae,
		2 Galdieria_sulphuralia,
		3 Porphyra_yezoensis,
		4 Porphyridium_purpureum,
		5 Neorhodella_cyanea,
		6 Dixoniella_grisea,
		7 Guillardia_theta,
		8 Pyrenomonas_helgolandii,
		9 Cryptomonas_ovata,
		10 Chroomonas_caudata,
		11 Aureococcus_anophagefferens,
		12 Heterosigma_akashiwo,
		13 Vaucheria_litorea,
		14 Vaucheria_frigida,
		15 Botrydium_granulatum,
		16 Fucus_distichus,
		17 Phaeodactylum_tricornutum,
		18 Chaetoceros_gracilis,
		19 Thalassiosira_pseudonana,
		20 Kryptoperidinium_foliaceum,
		21 Karlodinium_veneficum,
		22 Pavlova_lutheri,
		23 Karenia_brevis,
		24 Isochrysis_galbana,
		25 Emiliania_huxleii,
		26 Prymnesium_parvum,
		27 Heterocapsa_triquetra,
		28 Amphidinium_carterae;
	TREE PAUP_1 = ((((((1:36.0,2:31.0):9.0,3:23.0):7.0,(4:27.0,(5:17.0,6:11.0):6.0):7.0):7.0,((7:22.0,(8:12.0,9:22.0):7.0):10.0,10:26.0):6.0):17.0,(11:42.0,((12:27.0,(((17:10.0,20:7.0):5.0,18:18.0):7.0,19:18.0):15.0):6.0,((13:19.0,(14:9.0,15:9.0):6.0):6.0,16:31.0):18.0):11.0):6.0):0.0,(((21:27.0,(23:38.0,((24:12.0,25:9.0):8.0,26:9.0):8.0):8.0):19.0,22:47.0):12.0,(27:35.0,28:20.0):17.0):10.0);

END;