#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; 3:23 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 22581 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep22581;
        DIMENSIONS NTAX=19;
        TAXLABELS
            Arabidopsis_thaliana_AT5G59870.1
            Arabidopsis_thaliana_AT5G63470.2
            Phaseolus_vulgaris_Phvul.005G014300.2.p
            Phaseolus_vulgaris_Phvul.006G093200.4.p
            Phaseolus_vulgaris_Phvul.006G152400.1.p
            Phaseolus_vulgaris_Phvul.006G152500.1.p
            Phaseolus_vulgaris_Phvul.008G008900.1.p
            Phaseolus_vulgaris_Phvul.008G204500.1.p
            Phaseolus_vulgaris_Phvul.009G166000.1.p
            Phaseolus_vulgaris_Phvul.011G196500.1.p
            'Vigna unguiculata C35009181-augustus0.1'
            'Vigna unguiculata C35048311-processed0.1'
            'Vigna unguiculata C35084688-augustus0.5'
            'Vigna unguiculata scaffold12067-0.0'
            'Vigna unguiculata scaffold3280-processed0.1'
            'Vigna unguiculata scaffold42511-augustus0.4'
            'Vigna unguiculata scaffold44525-0.1_ORF+1'
            'Vigna unguiculata scaffold91373-0.1'
            'Vigna unguiculata scaffold91651-0.2_ORF+1'
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M43447]

	TITLE Cowpea_bean_CCAATHAP5_MAFFT;
	LINK TAXA = TaxaForAnalysisStep22581;
	DIMENSIONS NCHAR=291;
	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 ]
[                                                        .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         . ]
Arabidopsis_thaliana_AT5G59870.1                M---------------------------------------ESTGK-VKKAFGGRKPPGAPKTKSVSKSMKAGLQFPVGRITRFLKKGRYAQRLGGGAPVYMAAVLEYLAAEVLELAGNAARDNKKSRIIPRHLLLAIRNDEELGKLLSGVTIAHGG---------------------------------------------------------------------------------VLPNINSVLLPKKSATKPAE----EKATKSPVKSPKKA----------------
Arabidopsis_thaliana_AT5G63470.2                MD-NNNNNNNQQPPVYPSAVTTVIPPPPSGSASIVTHHLLQQQQQQLQMFW-------TYQRQEIEQVNDFKNHLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTDIFDFLVDIVPREEIKEEE----------------DAASALGG------------------------------------GGMVAPAASGVPYYYPPMGQPAVPGGMMIGRPAMDPSGVYA------QPPSQAWQS--VWQNSADDVSYGSS
Phaseolus_vulgaris_Phvul.005G014300.2.p         --------------------------------------------------------------------------FPAARIKKIMQADEDVGKIALAVPVLVSKALELFLQDLCDRTYEITLQRGAKTMNALHLKHCVQSYNVFDFLRDIVSRVPYGHGHGHFEGGADDRALSKRRKAAGVEGNESDEESKRSKMRELGHTGENFAAHEESTQSFRNIDLNANLNENEDKNASAAVQASVPE-PADMDIKHEEIPGWSLSEVDKMAIDTMQLATLGSRLEEDDEDYDEE---
Phaseolus_vulgaris_Phvul.006G093200.4.p         ----------QQ----------------------------HQLQQQLQQFW-------SSQYQEIEKVTDFKNHLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVDIVPRED-----------------------------------------------------------------------------------------------------------------------------------------
Phaseolus_vulgaris_Phvul.006G152400.1.p         ----------QQ----------------------------EKMQQRVNSFW-------ARQLKEIEESTDLKSHLPLARIRKIMKFDEDVKMVSTEATMLLAKACELFIMELTMRAWANVEDDKRRIIQKTDISSAISMSDVFDFLVDTVPRDD-----------------------------------------------------------------------------------------------------------------------------------------
Phaseolus_vulgaris_Phvul.006G152500.1.p         ----------QQ----------------------------EQLQEKVKNFW-------AQQLKRIEEGTDLRSRMPLSRIKKIMKSDPDVKLVSAETPVLFSKACELFIMELTMKAWANAENNSRGKIQKTDIASAIAGTEVFDFLDDIVPIPK-----------------------------------------------------------------------------------------------------------------------------------------
Phaseolus_vulgaris_Phvul.008G008900.1.p         --------------------------------------------------------------------------LPLARIRRIMKTDADVQMVSAETPMLMSKACEIFIQELTFRAWMRAEESNKSTVQPCDVAKVIMQNDALHFLTDIVPDNL-----------------------------------------------------------------------------------------------------------------------------------------
Phaseolus_vulgaris_Phvul.008G204500.1.p         -----------------------------------------------------------------------------------MQADEDVGKIAMAVPLLVSKALELFLQDLCDRTYEITLRRGAKTMNAFHLKQCVQTFNVFDFLKDIVSTGGRGRGRGRGRG--------------------------RGR-------------------GIRN--------------------------------KHDEYPGWSLSDMEKMTIDPIQLANINGRIDEDEEDYDEE---
Phaseolus_vulgaris_Phvul.009G166000.1.p         --------------------------------------LLHQQQQQLQMFW-------SYQRQEIEHVNDFKNHLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTDIFDFLVDIVPRDE-------------------------------------------------------------------LVGATASGVPYYYPPIGQPA---GMMIGRPAVDPTGVYV------QPPSQAWQS--VWQSAADDASY---
Phaseolus_vulgaris_Phvul.011G196500.1.p         --------------------------------------------------------------------------FPAARIKKIMQADEDVGKIALAVPVLVSKALELFLQDLCDRTYEITLQRGAKTMNSLHLKHCVQSYNVFDFLRDVVSRVPHGHGHGHAEAGADDRAISKRRKAVGDDGNDSDEEAKRGKMQEVSHTGENIAVPVVSTDSLRNIDLNAVTNENDDKKASVAADTSLPE-PPSTEVKHEEILGWPLSDVDKMAIDSTQLAQLARPLEEEEEDYDEE---
'Vigna unguiculata C35009181-augustus0.1'       -------HQQQQ----------------------------QQMQQRLQGFW-------TNQYQEIEKVTDF---LPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLR-------NKRKTLQKNDIAAAITRTDIFDFLVDIVPEDYKDEVL-----------------ASMPRGT---------------------------------------------------VPVTAP---------------------------------------------------
'Vigna unguiculata C35048311-processed0.1'      --------------------------------------------------------------------------FPVGRIARFLKAGKYAERVGAGAPVYLAAVLEYLAAEVLEL-------NKKTRIVPRHIQLAVRNDEELSKLLGDVTIANGG---------------------------------------------------------------------------------VMPNIHNLLLPKKAG----------GSSKGAG----------------------
'Vigna unguiculata C35084688-augustus0.5'       --------------------------------------------------------------------------FPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLEL-------NKKNRIVPRHIQLAVRNDEELSKLLGSVTIANGG---------------------------------------------------------------------------------VLPNIHQTLLPKKVG----------KGKGEIG----------------------
'Vigna unguiculata scaffold12067-0.0'           --------------------------------------------------------------------------DPVARIKKIMQADEDVGKIAMAVPLLVSKALELFLQDLCDREEEIFICNGTGTGFAI----------------------PY----------------------------------------------------------------------------------------------------------------------------------------
'Vigna unguiculata scaffold3280-processed0.1'   -------HQQQQ----------------------------DQMEEKVKSFW-------AQQRKEIEESTDI---VPLSRIKKIMKTDPDVKLVAAETPVVFSKACELFIMELTMK-------NNRRTIKKCDIASAIAKTDVFDFLDDIAP--------------------------------------------------------------------------------------------------------------------------------------------
'Vigna unguiculata scaffold42511-augustus0.4'   FPVGKKGRYAQRAPVYLAAVLEYLAAELNKKNRIIPRHLDEELGKLVTIAHGGVLPNINPGSDDTGGKIKKGAGFPVGRIGRYLKKGRYAQRVGTGAPVYLAAVLEYLAAEVLEL-------NKKNRIIPRHVLLAVRNDEELGKLLAGVTIAHGG---------------------------------------------------------------------------------VLPNINPVLLPKKTE----------KASKEPK----------------------
'Vigna unguiculata scaffold44525-0.1_ORF+1'     VAAGANQHHQQQ----------------------------QHQQQQLQMFW-------SNQMQEIDQTIDF---LPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLR-------NKRRTLQKNDIAAAISRNDVFDFLVDIIPKEEGLGIT----------------KATIPLVG------------------------------------------SPADMPYYYVPPQHPAGPPGMIMGKP-VDQAALYSTQPRPQQPPQQQQQQ--QQQTDS--------
'Vigna unguiculata scaffold91373-0.1'           -------QYYPQ----------------------------NIQEGKLRSFW-------EKQLLDIEAAEAF---LPLARIRRIMKTDADVQMVSAETPMLMSKACEIFIQELTFR-------SNKSTVQPCDVAKVIMQNNAMQFLTEIVPNFCAGAQEGKLRSFWEKQLLDIEAEAFLPLAR---------------------------------------IRRMKTDADVQMVSAETP-----MLMSKAFIQELTFRS-NKSTVQPCDVAKVI--MQNNAMQFLTEIVP
'Vigna unguiculata scaffold91651-0.2_ORF+1'     --------------------------------------------------------------------------FPAARIKKIMQADEDVGKIALAVPVLVSKALELFLQDLCDR-------RGAKTMNALHLKHCVQSYNVFDFLRDIVSRVPYGHGHGHSEAGADDRALSKRRKAAGVEGNESDEEAKRSKMRELGHAGETSAVHEESAQSFRNIDLNANINENEDKNAGAAVEASLPE-PSDMDIKH-EVPGWSLSDVDKMAIDTMQLATLGSRLEEDDEDYDEEG--
;
END;

[ The following blocks are output data for analysis step 22581 ]
BEGIN TREES;
      TITLE Cowpea_bean_CCAATHAP5;
      LINK TAXA = TaxaForAnalysisStep22581;
      TREE Cowpea_bean_CCAATHAP5 = [&R] (((Phaseolus_vulgaris_Phvul.011G196500.1.p:0.21314765568819907,('Vigna unguiculata scaffold91651-0.2_ORF+1':0.03778385231398585,Phaseolus_vulgaris_Phvul.005G014300.2.p:0.018948808620755455):0.06937899972659858):0.25612184281979333,'Vigna unguiculata scaffold12067-0.0':0.6730452224469364):0.10599734687287131,(((Phaseolus_vulgaris_Phvul.006G152400.1.p:0.10927781367958533,((Phaseolus_vulgaris_Phvul.006G152500.1.p:0.17191221441554078,'Vigna unguiculata scaffold3280-processed0.1':0.1876420641537606):0.1419990249879908,('Vigna unguiculata scaffold91373-0.1':0.24088860178061863,Phaseolus_vulgaris_Phvul.008G008900.1.p:1.00000050002909E-6):0.9536909407121897):0.2312448472051121):1.00000050002909E-6,('Vigna unguiculata C35009181-augustus0.1':1.00000050002909E-6,(Phaseolus_vulgaris_Phvul.006G093200.4.p:1.00000050002909E-6,((Phaseolus_vulgaris_Phvul.009G166000.1.p:0.0035708815153217923,Arabidopsis_thaliana_AT5G63470.2:0.03796189668089187):0.31912865707402704,'Vigna unguiculata scaffold44525-0.1_ORF+1':0.321437969042449):0.14159637683781215):0.17791136785001002):0.5711522446090285):0.88912133647711,(('Vigna unguiculata C35048311-processed0.1':0.2119292684327988,'Vigna unguiculata C35084688-augustus0.5':0.2287306067720738):1.00000050002909E-6,(Arabidopsis_thaliana_AT5G59870.1:0.542516731313777,'Vigna unguiculata scaffold42511-augustus0.4':0.31693863978400144):0.21839906252407698):3.519495387445006):2.1703501623479124,Phaseolus_vulgaris_Phvul.008G204500.1.p:1.00000050002909E-6)OROOT;
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr107967]


END;