#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 December 27, 2025; 3:26 GMT

TreeBASE (cc) 1994-2008

Study reference:
Misra V.A., Wang Y., & Timko M.P. 2017. A Compendium of Transcription Factor and
Transcriptionally Active Protein Coding Gene Families in Cowpea (Vigna unguiculata
L.). BMC Genomics, .

TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S21817]

[ The following blocks are input data for analysis step 22572 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep22572;
        DIMENSIONS NTAX=15;
        TAXLABELS
            Arabidopsis_thaliana_AT1G76900.1
            Arabidopsis_thaliana_AT2G47900.1
            Phaseolus_vulgaris_Phvul.003G100700.1.p
            Phaseolus_vulgaris_Phvul.004G095000.1.p
            Phaseolus_vulgaris_Phvul.006G210500.1.p
            Phaseolus_vulgaris_Phvul.007G079900.1.p
            'Vigna unguiculata C35035869-processed0.0'
            'Vigna unguiculata scaffold16727-processed0.1'
            'Vigna unguiculata scaffold17614-processed0.2'
            'Vigna unguiculata scaffold2073-augustus0.1'
            'Vigna unguiculata scaffold4198-0.2'
            'Vigna unguiculata scaffold76540-0.2'
            'Vigna unguiculata scaffold82703-processed0.0'
            'Vigna unguiculata scaffold84934-0.2'
            'Vigna unguiculata scaffold87500-0.1'
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M43431]

	TITLE Cowpea_bean_TUB_MAFFT;
	LINK TAXA = TaxaForAnalysisStep22572;
	DIMENSIONS NCHAR=477;
	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        100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       ]
[                                                         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .       ]
Arabidopsis_thaliana_AT1G76900.1                 -------------------------------------------------------------MSFRSIVRDV--RDSIGSLSRRSFDFKLSSG--GKSRGSVQDSEQLVVTIQETPWANLPPELLRDVIKRLEESESVWPARRHVVACASVCRSWRDMCKEIVQSPELSGKITFPVSLKQPGPRDATMQCFIKRDKSNLTYHLYLCLSPALLVENGKFLLSAKRIRRTTYTEYVISMHADTISRSSNTYIGKIRSNFLGTKFIIYDTQPAYNSNIVQPVGLSRRFYSKRVSPKVPSGSYKIAQVSYELNVLGTRGPRRMHCAMNSIPASSLAEGGTVPGQPDIIVSILDSFRSITSSSSRDYSNDFSSARFSDILGPLSDEEGKERPLVLKNKPPRWHEQLQCWCLNFRGRVTVASVKNFQLIAALTQPQPSGQDKIILQFGKVGKDMFTMDFRYPLSAFQAFAICLSSFDTKLACE-
Arabidopsis_thaliana_AT2G47900.1                 -------------------------------------------------------------MSFKSLIQDM--RGELGSISRKGFDVRFGYG-RSRSQRVVQDTSVPVDAFKQSCWASMPPELLRDVLMRIEQSEDTWPSRKNVVSCAGVCRNWREIVKEIVRVPELSSKLTFPISLKQPGPRGSLVQCYIMRNRSNQTYYLYLGLNQAASNDDGKFLLAAKRFRRPTCTDYIISLNCDDVSRGSNTYIGKLRSNFLGTKFTVYDAQPTNPGTQVTRTRSSRLLSLKQVSPRIPSGNYPVAHISYELNVLGSRGPRRMQCVMDAIPASAVEPGGTAPTQTELVHSNLDSFPSFSFFRSK-------SIRAESLPSGPSSAAQKEGLLVLKNKAPRWHEQLQCWCLNFNGRVTVASVKNFQLVAAPENGAGPEHENVILQFGKVGKDVFTMDYQYPISAFQAFTICLSSFDTKIACE-
Phaseolus_vulgaris_Phvul.003G100700.1.p          --------------------------------------------------------------------------------------------------------------LEQSWWANMPHELLREVLLRIESSEAKWPPRRSVVACAGVCRTWRLIVKEIVKPPQLSSNITFPISLKQPGPREHLLQCFIRRNSGTQTYYLFLSLSSA-LADDGKFLLAARKFRRPTCTDYIISLDADDMSRESSAHIGKLRSNFLGTKFTIYDSQLPHARA---------LVNPKQVSPKVPTGNYPVAHISYELNVLGSRGPRRMHCVIDTIPASAIEPERVAPSQ---------------------------------------------------NKAARWHEQMQCWCLNFQGRVTIASVKNFLAALTVNGHAEPQEDDVILQFGKVGKDMFTMDYRYPISAFQAFAICLSSFATTVACE-
Phaseolus_vulgaris_Phvul.004G095000.1.p          --------------------------------------------------------------SFRSIVRDV--RDGIGSLSRRSFDLR----------------------IQNSRWASLPPELLRDVIRRLEESETTWPARKHVVACAAVCKSWREMCKEIVTSPEFCGKITFPVSLKQPGSRDGAIQCFIKRDKSNLTYHLFLCLSPA-LVENGKFLLSAKRTRRTTCTEYTISMDADNISRSSNTYIGKLRSNFLGTKFIIYDTQPPYNNT---------RFNSKKVSPKVPSGSYNIAQITYELNVLGTRGPRRMNCSMHSIPVSALEPGGTVPGQED-------SFRSISFARSIYSSTEFSSSRFSDIVVAG---NEEEQGKDMPNKAPRWHEQLQCWCLNFRGRVTVASVKNFAPPPPSSQPAQSDHDKIILQFGKVGKDIFTMDYRYPLSAFQAFAICLTSFDTKLACE-
Phaseolus_vulgaris_Phvul.006G210500.1.p          --------------------------------------------------------------SFRSIVRDV--RDSFGSLSRRSFDLR----------------------IQNSRWASLPPELLFDIIRRLEESENTWPSRKHVVACAAVCQSWRNMCKEIVKSPEFCGKLTFPVSLKQPGPRDGIIQCFIKRDKSNLTYHLFLCLSPA-LVENGKFLLSAKRTRRTTYTEYVISMDADNISRSSNTYIGKLRSNFLGTKFIINDTQPPYSSA---------RFYSKKVSPKVPSGSYNIAQVTYELNVLGTRGPRKMHCVMHSIPASALDAGGTVPGQED-------SFRSISFSKSLDRSIEFSSSRFSEIGESC---LEDDDGKMRPNKPPRWHEQLQCWCLNFRGRVTVASVKNFAGAPTPSQPAPPEHDKIILQFGKVGKDMFTMDYRYPLSAFQAFAICLSSFDTKLACE-
Phaseolus_vulgaris_Phvul.007G079900.1.p          --------------------------------------------------------------SFRSIVRDV--RDGFGSLSRRSFEVR----------------------IQNSRWASLPPELLRDVINRLEASESTWPGRKHVVACAAVCKSWREMCKEIVSSPELCGKITFPIALKQPGHRNGTIQCFIKREKSKLTYHLFLCLSPA-LVENGKFLLSAKRTRRTTCTEYIISMDADNISRSSSTYIGKLRSNFLGTKFIIYDTQPPYNNA---------RRFSKKVSPKVPSGSYNIGQVTYELNVLGTRGPRRMNCTMYSIPASSLEPNGVVPGQED-------SFRSISFSKSIDNSTRFSSSRFSDIMGTG---SEDQEGKVVPNKSPRWHEQLQCWCLNFRGRVTVASVKNFPTLSHPPQSSSSDHDKIILQFGKVGKDMFTMDYRYPLSAFQAFAICLTSFDTKLACE-
'Vigna unguiculata C35035869-processed0.0'       --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ENGKFLLSAKRTRRTTYTEYVISMDADNISRSSNTYIGKLRSNFLGTKFIIYDTQPPYSSAHICPPGTGKRFYSKKVSPKVPSGSYNIAQVTYELNVLGTRGPRKMHCVMHSIPASALDAGGTVPGQPELLPRSL---------------------------------EGKLRPLVLKNKPPRWHEQLQCWCLNFRGRVTVASVKNFQLIAA-----------IILQFGKVGKDMFTMDYRYPLSAFQAFAICLSSFDTKLACE-
'Vigna unguiculata scaffold16727-processed0.1'   -------------------------------------------------------------MSFRSII-----------VERKGFEFKFGYSMRSRSQSIAQDRLVVPD--KQSCWANMPPELLRDVLMRIEASEDSWPARKHVVACAGVCRSWREIMKEIVKSPQVSGNLTFPISLKQPGPRGSLLQCYIKRNHSNKTYYLFLGLNQ----EDGKFLLSARKCRRATHTDYIISLNCEDVSRGSDTYIGKLRSNFLGTKFTVYDAHPPIYGAKVTKSRSTRLVSLKQVSPRVPAGNYPIAHVSYDLNVLGSRGPRIMHCVMDAIPASAVEPGGVAPTQTQFLHSRID--------RSK-------STRMDSLTSAP---LQNEGMLVLQNKSPRWHEQLQFWCLNFNGRVTVASVKNFQLVASPKNGVSEQAQEVILQFGKVGKDVFTMDYQYPISAFEAFAICLSSFDTKIACE-
'Vigna unguiculata scaffold17614-processed0.2'   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DMSKLLLAAKKIRRATCTEFLISLVADDFSRTSNTYIGKLRSNFLGTKFMILDGESPHDSSLPLNCKLQQRVHLKQVLVAAAAANYKVATVSYELNVLRTRGPRRMRCTMHLIPISAIQEGGSAPTPLKFTNYLN---------------------------------ERAREPLVLKNKAPRWHEQLQCWCLNFKGRVTVASVKNFQLVAAPCQNVSAAEHEVILQFGKIGKDIFTMDYRYPLSAFQAFAICLSSFDTKPDNL-
'Vigna unguiculata scaffold2073-augustus0.1'     ---------------------------------------------------------------------------------------------------------------EQSWWANMPHELLREVLLRIESSEAKWPRRRTVVACAGVCRTWRLIIKEIVKPPQLSSNITFPISLKQPGPREHLLQCFIRRNSGTQTYYLFLSLSS----DDGKFLLAARKFRRPTCTDYIISLDADDMSRESNAYIGKLRSNFLGTKFTIYDSQLPHARAKMTKSCSTKLVNPKQVSPKVPIGNYPVAHVSYELNVLGSSTTYHILCVIDSIPASAIEPEWVAPSQTSYSVSNI---------------------------------GKTDDVLVLRNKAARWHEQMQCWCLNFHGRVTVASVKNFQLAAL-----------VILQFGKVGKDLFTMDYRYPISAFQAFAICLSSFATTVACE-
'Vigna unguiculata scaffold4198-0.2'             -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SNFLGTKFTIYDSQPPHDAAIQQNCQSSRRFHSKQVSPRVPACSYLVSTVSYELNVLCTRGPRRMHCVMNSIPVSAIQEGGNAPTPTSFPQIFDE-FSPSPAAKEKVPVPDLNSASLSEPLIST---QVSTEQLELKNKAPRWHEQLQCWCLNFKGRVSVASVKNFQLVAAPSHNVSAEEQDVILQFGKIGKDIFTMDYRYPLSTFQAFAICLSSFDTKPACE-
'Vigna unguiculata scaffold76540-0.2'            --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DKGKFLLAARRYRCGTHTEYIISLDADDLSQGSNAYVGKLSSDFLGTNFTIYDSQPPHSGAKPSSGRASRRFASKQISPQVPAGNFEVGQVSYKFNLLKSRGPRRM-----------------VPTGETSDSTSLD------------------GHKMHD---KE---HFASGHTILKNKAPRWHEHLQCWCLNFHGRVTVASVKNFQLVAT-----------VLLQFGKVGDDTFTMDYRQPLSAFQAFAICLTSFGTKLACE-
'Vigna unguiculata scaffold82703-processed0.0'   -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SNFLGTKFIIYDTQPPYNNSQLSPPGRSRRFNSKKVSPKVPSGSYNIAQITYELNVLGTRGPRRMNCTMHSIPVSALEPGSTVPGQPELLPRAL---------------------------------EGKDMPLVLKNKAPRWHEQLQCWCLNFRGRVTVASVKNFQLIAA-----------IILQFGKVGKDIFTMDYRYPLSAFQAFAICLTSFDTKLACE-
'Vigna unguiculata scaffold84934-0.2'            MGIIRSMRSRSHRVVQEQEECRQSCWANMPQELLREVLLRIEASEDTWPPRKSVVACAGVCRSWRQITKDIVKTPELSSISVKQMGIR---SMRSRSHRVVQEQ----EECRQSCWANMPQELLREVLLRIEASEDTWPPRKSVVACAGVCRSWRQITKDIVKTPELSSKITFPISVKQPGPRENLLRCFIKRNRSTQTYYLFLSLTNEDRIEDGKFLLAARKCRRPTCTDYIISLDADDMSKGSNSYVGKLRSNFLGTKFTIYDSQPPHSGARIMKSRSTRLVNLKQVSPKVPTGNYPVAHISYELNVLGSRGPRRMHCVMDSIPATAIEAGGVAPTQTEFSLNNID--------RSK-------SNRVENTMSGP---LQKDGMLVLKNKSPRWHEQLQCWCLNFHGRVTIASVKNFQLVAS-----------IILQFGKVGKDLFTMDYRYPISAFQAFAMCLSSFDTKIACE-
'Vigna unguiculata scaffold87500-0.1'            KSIVRELKSMSKRGVESRRDLQQGQWANLPPELLLDIISRVEESETTWPARAVVVHCGSVCVTMKSIVRELKERDGIGSMSKRGVESRRWNG-RTKSY-VAPD--ITLTSLQQGQWANLPPELLLDIISRVEESETTWPARAVVVHCGSVCKSWRDVTKEIAKTPEQCGRITFPISLKQPGPRDSPIQCFIRRNRETSTYLLYIGLVP----ETDKLLLAAKKVRRATGTDFIVSLVADDFSRSSNTYVGKLKSNFLGTKFTVYDSQPPQGAAIQQDSGSSRRFHSKQSSPKVSAFNYVVGTIAYELNVLRARGPRRMHCTMNSIPISAIQEGGTAPTPTSFPQIIDR-FSPSPALKGKGSSTDLNNVNLPKLAVPG---QGSSEPMVLKNKAPRWHEQLQCWCLNFKGRVTVASVKNFQLVAAPSHNVSAAEQ-----------------------------------------E-
;
END;

[ The following blocks are output data for analysis step 22572 ]
BEGIN TREES;
      TITLE Cowpea_bean_TUB;
      LINK TAXA = TaxaForAnalysisStep22572;
      TREE Cowpea_bean_TUB = [&R] ((Phaseolus_vulgaris_Phvul.006G210500.1.p:0.10365550605353996,Phaseolus_vulgaris_Phvul.007G079900.1.p:0.07818973618193728):0.009659131097564317,(((('Vigna unguiculata scaffold17614-processed0.2':0.2766202693700917,('Vigna unguiculata scaffold4198-0.2':0.11506815253332058,'Vigna unguiculata scaffold87500-0.1':0.1563533228706299):0.08803521570453864):0.3454495279414011,(((Arabidopsis_thaliana_AT2G47900.1:0.11290878893808115,'Vigna unguiculata scaffold16727-processed0.1':0.16871695355229457):0.1181078189496298,((Phaseolus_vulgaris_Phvul.003G100700.1.p:0.05471614753614138,'Vigna unguiculata scaffold2073-augustus0.1':0.10954802035244755):0.18596334191335714,'Vigna unguiculata scaffold84934-0.2':0.12881375734939987):0.10932452259153644):0.25044183918075713,'Vigna unguiculata scaffold76540-0.2':0.44797158007290827):0.08755942678439481):0.21217422114212778,'Vigna unguiculata scaffold82703-processed0.0':0.04270525257402498):0.038588715398324334,(Arabidopsis_thaliana_AT1G76900.1:0.1573615612152759,'Vigna unguiculata C35035869-processed0.0':0.031997933463079414):0.031070303673520774):0.08165793846096875,Phaseolus_vulgaris_Phvul.004G095000.1.p:0.03826338816002382)OROOT;
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr107963]


END;