#NEXUS

BEGIN TAXA;
	TITLE TaxaForAnalysisStep8996;
	DIMENSIONS NTAX=19;
	TAXLABELS
		Ambystoma_mexicanum_tbx5 Anolis_carolinensis_tbx5 Danio_rerio_tbx5a Danio_rerio_tbx5b Gallus_gallus_tbx5 Gasterosteus_aculeatus_tbx5a Gasterosteus_aculeatus_tbx5b Homo_sapiens_tbx5 Monodelphis_domestica_tbx5 Notophthalmus_viridescens_tbx5 Oryzias_latipes_tbx5a Oryzias_latipes_tbx5b Silurana_tropicalis_tbx5 Taeniopygia_guttata_tbx5 Takifugu_rubripes_tbx5a Takifugu_rubripes_tbx5b Tetraodon_nigroviridis_tbx5a Tetraodon_nigroviridis_tbx5b Xenopus_laevis_tbx5 
	;

END;


BEGIN CHARACTERS;
	TITLE  Parrie_et_al_tbx5_alignment;
	DIMENSIONS  NCHAR=311;
	FORMAT DATATYPE = Protein GAP = - MISSING = ?;
	MATRIX
	Ambystoma_mexicanum_tbx5        --------------------------------------------------QGMEGIKVFLHERELWLKFH-EVGT-EMVITKAGRRMFPSYKVKVTGLNPKTKYILLMDIVPADDHRYKFADNKWSV--TGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFSETAFIAVTSYQNHKITQLKIENNPFAKGFRGSDDMELHRMSRMQS-KEYPVVPRSTVRQKV-------------------------------------
	Anolis_carolinensis_tbx5        MADAEEGFGLPTTPVEADTKELGGEGKAEGPATGTPSKPPASPQAAFT-QQGIEGINIFLDPCALHLCLACATGTNDPSFSSLGRRMFPSYKVKVTGLNPKTKYILLMDIVPSDDHRYKFADNKWSV--TGKAEPAMPGRLYVHPDSPATGAHWMRQLVSSRKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFAETAFIAVTSYQNHKITQLKIENNPFAKGFRGSDDMELHRMSRMQS-KEYPVVPRSTVRQKVYHCTKRKHPYKKPYMETSPQEDDSFYRSQRQACMYAS
	Danio_rerio_tbx5a               MADSEDTFRLQNSPSDSEPKDLQNEGKSDKQNAAVSKSP--SSQTTYI-QQGMEGIKVYLHERELWTKFH-EVGT-EMIITKAGRRMFPSFKVKVTGLNPKTKYILLMDVVPADDHRYKFADNKWSV--TGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRIHIVKADENNGFGSKNTAFCTHVFPETAFIAVTSYQNHKITQLKIENNPFAKGFRGSDDMELHRMSRMQSTKEYPVVPRSTVRQRVYHCIKRKHPYKKPYVESSSSEDDHYYRPQRQACMYAS
	Danio_rerio_tbx5b               MANPMFESLRACSGGNSPAMDFERDKDSGHHGRNKTGSPP--LQTQLS-QQSMEGIKVYLHEKDLWAKFH-DVTT-EMIITKAGRRMFPSYKVKVTGLNPKAKYILLMDIISADEHRYKFADNKWSI--SGKAEPAIPGRLYVHPDSPASGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADERNSFGSSNTSFCTHSFAETTFIAVTSYQNHTITQLKIENNPFAKGFRGNDDIELHRMSRTPS-KEYPLVPRSTARQRAFTCSDTS-------LTETPSIHDPTYPLQHQPCMYGG
	Gallus_gallus_tbx5              MADTEEGFGLPSTPVDSEAKELQAEAKQDPQLGTTSKAPT-SPQAAFT-QQGMEGIKVFLHERELWLKFH-EVGT-EMIITKAGRRMFPSYKVKVTGLNPKTKYILLMDIVPADDHRYKFADNKWSV--TGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFPETAFIAVTSYQNHKITQLKIENNPFAKGFRGSDDMELHRMSRMQS-KEYPVVPRSTVRQKVYHCTKRKHPYKKPYMETSPAEEDPFYRSQRQACMYAS
	Gasterosteus_aculeatus_tbx5a    MADQEETFALENSPGGSESRELQSDNKSEKQNGTSSKSP--SSQTTYI-QQGMEGIKVYLHERELWIKFD-EVGT-EMIITKAGRRMFPSFKVKVTGLNPKTKYILLMDVVPADDHRYKFADNKWSV--TGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRIHIVKADENNGFGSKNTAFCTHVFPETAFIAVTSYQNHKITQLKIENNPFAKGFRGSDDMELHRMSRMQSTKEYPVVPRSTVRQRVYHCIKRKQSYKKAYLESSSSEEDHYYRPQRQACMYAS
	Gasterosteus_aculeatus_tbx5b    MANGGDQFGLAERP-DSHCMDSPKEAKQKHS-SYTLDSPA-SPQKASS-QPGMEGIKVFLHDRELWTKFD-GVGT-EMIITKAGRRMFPSYKVKVTGLNPKTKYILLMDIVPGDDHRYKFADNKWSI--TGKAEPAMPGRLYVHPDSPATGAHWSRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFSETAFIAVTSYQNHKITQLKIENNPFAKGFRGSDDNELHRMAKLQG-RMTSCCCGSAQRLRVFLCLHPSHPFKKCFTGRSSSEGESYY--QRQACMFAG
	Homo_sapiens_tbx5               MADADEALAGAHLWSLTQKTCLRFEPRAR---SGPPASPPGRPRSRLH-PAGMEGIKVFLHERELWLKFH-EVT--EMIITKAGRRMFPSYKVKVTGINPKTKYILLMDIVPADDHRYKFADNKWCV--TGKAEPAMAGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFPETAFIAVTSYQNHKITQLKIENNPFAKGFRGSDDMELHRMSRMQS-KEYPVVPRSTVRQKVYHCTKRKHPYKKPYMETSPSEEDSFYRSQRQACMYAS
	Monodelphis_domestica_tbx5      MADADEAFGLPHTPLEAESKELPPEAKQENPLGSSSKAPA-SPQAAFT-QQGMEGIKVFLHERELWLKFH-EVGT-EMIITKAGRRMFPSYKVKVTGLNPKTKYILLMDIVPADDHRYKFADNKW?AWGAGRTEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFPETAFIAVTSYQNHKITQLKIENNPFAKGFRGSDDMELHRMSRMQS-KEYPVVPRSTVRQKVYHCTKRKHPYKKPYMETSPTEEDPFYRSQRQACMYAS
	Notophthalmus_viridescens_tbx5  MADSDEGFGMPDTPVDPESKELQSDSKQDSQLGAGSKPPS-SPQAAFT-QQGMEGIKVFLHERELWLKFH-DVGT-EMIITKAGRRMFPSYKVKVSGLNPKTKYILLMDIVPADDHRYKFADNKWSV--TGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFSETAFIAVTSYQNHKITQLKIENNPFAKGFRGSDDMELHRMSRMQS-KEYPVVPRSTVRQKVYHCTKRKHTYKKSYMETSPTEEDPFYRSQRQACMYAS
	Oryzias_latipes_tbx5a           MADQEETFVLQNSPGSSDTREIQSDNKPEKQNGTSSKSP--SSQTTYIQQVGKR?IKVYLHERELWMKFH-EVGT-EMIITKAGRRMFPSFKVKVTGLNPKTKYILLMDVVPADDHRYKFADNKWSV--TGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRIHIVKADENNGFGSKNTAFCTHVFPETAFIAVTSYQNHKITQLKIENNPFAKGFRGSDDMELHRMSRMQSTKEYPVVPRSTVRQRVYHCIKRKHSYKKAFLESSSSEDDHYYRPQRQACMYAS
	Oryzias_latipes_tbx5b           MANGGEQFGLAEHP-DPGCVDSPEEPKLENP-RLNLSSAN-SPQTASS-QQGMGSIKVVLHDRELWTKFD-EVGT-EMIITKAGRRMFPSYKVKVIGLNPKTKYILLMDIVPGDDHRYKFADNKWSV--TGKAEPAMPGRLYVHPDSPATGAHWSRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFPETAFIAVTSYQNHKITQLKIENNPFAKGFRGSDDNELHRMAKLQG-KDYPVVPRSTVRQRSYNCSKRKHAYKKTFNSGSPSGTESYCHPQRQACMFAS
	Silurana_tropicalis_tbx5        MADTEEAYGMPDTPVEPEPKELQCEPKQDNQMGASSKTPT-SPQAAFT-QQVREVIHIYVHEEMYAFKFY-KRMT-ELLIKRAGRRMFPSYKVKVTGLNPKTKYILLMDIVPADDHRYKFADNKWSV--TGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFSETAFIAVTSYQNHKITQLKIENNPFAKGFRGSDDMELHRMSRMQS-KEYPVVPRSTVRQKVYHCTKRKHSYKKPYMDTSPSEEDPYYRSQRQACMYAS
	Taeniopygia_guttata_tbx5        MADGEEGFGLPGTPADSEAKELQAEGKQDTQLGATSKSPT-SPQAAFT-QQGMEGIKVFLHERELWLKFH-EVGT-EMIITKAGRRMFPSYKVKVTGLNPKTKYILLMDIVPADDHRYKFADNKWSV--TGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYRPKMHLSP--------------CLHSL----------WKYLPITQLKIENNPFAKGFRGSDDMELHRMSRMQS-KEYPVVPRSTVRQKVYHCTKRKHPYKKPYMETSPADEDPFYRSQRQACMYAS
	Takifugu_rubripes_tbx5a         MADQEETFGLQNSPSGSDSRDLPNDNNKSEKQNGTSSKSP-SSQTTYI-QQGMEGIKVYLHERELWTKFY-EVGT-EMIITKAGRRMFPSFKVKVTGLNPKTKYILLMDVVPADDHRYKFADNKWSV--TGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRIHIVKADENNGFGSKNTAFCTHVFPETAFIAVTSYQNHKITQLKIENNPFAKGFRGSDDMELHRMSRMQSTKEYPVVPRSTVRQRVYHCIKRKHSYKKAYMDSSSSEEDHYYRPQRQACMYAS
	Takifugu_rubripes_tbx5b         MANGGDQFGLSDPP-NSDCMDSPKETKQEKQ-SYALNSPA-SPHTTSTQQQGMEGIKVFLHDRDLWTKFD-EVGT-EMIITKAGRRMFPGYKVKVTGLNPKTKYILLMDIVPGDDHRYKFADNKWSV--TGKAEPAMPGRLYVHPDSPATGAHWSRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFPETAFIGVTSYQNHKITQLKIENNPFAKGFRGSDDNELHRMAKLQS-KDFPVVPRTAGRQRAYHCPERKHPYKKLFPGSSPSESDSYYHPGRQACMFAG
	Tetraodon_nigroviridis_tbx5a    MADQEETFGLQNSPSGSDSRDLQNDNNKSEKQNGTSSKSP-SSQTTYI-QQGMEGIKVYLHERELWTKFY-EVGT-EMIITKAGRRMFPSFKVKVTGLNPKTKYILLMDVVPADDHRYKFADNKWSV--TGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRIHIVKADENNGFGSKNTAFCTHVFPETAFIAVTSYQNHKITQLKIENNPFAKGFRGSDDMELHRMSRMQSTKEYPVVPRSTVRQRVYHCIKRKHSYKKAYMDSSSSEEDHYYRPQRQACMYAS
	Tetraodon_nigroviridis_tbx5b    MANGGDQFGLSEPP-NSDCMDSPKEAKEEKQ-SYALDSPA-SPQTIFS-QQGMEGIKVFLHDRDLWTRFD-EVGT-EMIITKAGRRMFPGYKVKVVGLNPKTKYILLMDIVPGDDHRYKFADNKWSV--TGKAEPAMPGRLYVHPDSPATGAHWSRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFPETTFIAVTSYQNHKITQLKIENNPFAKGFRGSDDNELHRMAKLQS-KDFPVVPRSAVRQSAYRCPERKHPYKKLFPASSPSECDSYYHPQRQACMFAG
	Xenopus_laevis_tbx5             MADTEEAYGMPDTPVEAEPKELQCEPKQDNQLGASSKTPT-SPPAAFT-QQGMEGIKVFLHERELWLKFH-EVGT-EMIITKAGRRMFPSYKVKVTGLNPKTKYILLMDIVPADDHRYKFADNKWSV--TGKAEPAMPGRLYVHPDSPATGAHWMRQLVSFQKLKLTNNHLDPFGHIILNSMHKYQPRLHIVKADENNGFGSKNTAFCTHVFSETDFIAVTSYQNHKITQLKIENNPFAKGFRGSDDMELHRMSRMQS-KEYPVVPRSTVRQKVYHCTKRKHSYKKPYMDTSPSEEDPFYRSQRQACMYAS

;


END;

BEGIN TREES;
	Title Parrie_et_al_tbx5_result;
	LINK Taxa = TaxaForAnalysisStep8996;
	TRANSLATE
		1 Ambystoma_mexicanum_tbx5,
		2 Anolis_carolinensis_tbx5,
		3 Danio_rerio_tbx5a,
		4 Danio_rerio_tbx5b,
		5 Gallus_gallus_tbx5,
		6 Gasterosteus_aculeatus_tbx5a,
		7 Gasterosteus_aculeatus_tbx5b,
		8 Homo_sapiens_tbx5,
		9 Monodelphis_domestica_tbx5,
		10 Notophthalmus_viridescens_tbx5,
		11 Oryzias_latipes_tbx5a,
		12 Oryzias_latipes_tbx5b,
		13 Silurana_tropicalis_tbx5,
		14 Taeniopygia_guttata_tbx5,
		15 Takifugu_rubripes_tbx5a,
		16 Takifugu_rubripes_tbx5b,
		17 Tetraodon_nigroviridis_tbx5a,
		18 Tetraodon_nigroviridis_tbx5b,
		19 Xenopus_laevis_tbx5;
	TREE tree_1 = (((9:0.049293873386243914,(2:0.20885639239424836,8:0.19897912629267434):0.018618958301764743):0.022490841207102985,((5:0.009533239476471667,14:0.0922401713986718):0.023332648141668466,(10:0.05547453645104705,((19:0.010038119678407842,13:0.09856464606855919):0.005655549961381068,1:0.010063056620589261):0.02573819291809254):0.021228390157556953):0.006566042799947769):0.03328576986023083,((((18:0.04563566547232062,16:0.037149308841701145):0.044803189805554255,(12:0.15844596075686662,7:0.1708566758371583):0.018165961479919945):0.17964553193057542,4:0.5738665714786199):0.04323240700357045,(3:0.030405315682814127,((17:1.2830841978339613E-6,15:0.0036677920127726193):0.06014128026806054,(11:0.044625841617619455,6:0.014110035016976608):0.0280200677883376):0.03104249481573651):0.07358959316273861):0.03328576986023087);

END;