#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 22582 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep22582;
        DIMENSIONS NTAX=7;
        TAXLABELS
            Arabidopsis_thaliana_AT1G19350.1
            Arabidopsis_thaliana_AT2G45880.1
            Phaseolus_vulgaris_Phvul.001G016050.2.p
            Phaseolus_vulgaris_Phvul.002G026800.2.p
            Phaseolus_vulgaris_Phvul.008G065600.1.p
            'Vigna unguiculata scaffold30811-0.2'
            'Vigna unguiculata scaffold56985-augustus0.2'
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M43448]

	TITLE Cowpea_bean_BES_MAFFT;
	LINK TAXA = TaxaForAnalysisStep22582;
	DIMENSIONS NCHAR=730;
	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       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730]
[                                                        .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .]
Arabidopsis_thaliana_AT1G19350.1                MTS-------------------------DGATSTSAAAAAA----------------------AMATRRKPSWRERENNRRRERRRRAVAAKIYTGLRAQGNYNLPKHCDNNEVLKALCSEAGWVVEEDGTTYRKG-HKPLPGDMAGSS----SRATPYS-SHNQSPLSSTFDSPILS-YQVS---------PSSS-----SFPSPSRVG-----------------DPHNISTIF---------------PFLRNGGIPSSLPPLRISNSAPVTPPVSSPTSRNPKPLPTWESFTKQSMSMA-AKQSMTSLNYPFYAVSAPASPTH-----HRQFHA-----------PATIPEC--DESDSSTVDSGHWI----------------------------------------------------SFQKFAQQQPFSASMVPTSPTFNLVKPAPQQLS------------------------------------PNTAAIQEIGQSSEFKFENSQVKP----------------------WEGERI------------------------------HDVAMEDLELTLGNGK-------------------------------------------------------------------------------------------------------------------------AHS---------------
Arabidopsis_thaliana_AT2G45880.1                MATDMHKLLGTSEEDDDEEMDMDVKEEDDGDRRNRDKHAASGSSSNDEFMFQQSMQDQVGTPGGGGSRRSRPLEEKERTKLRERHRRAITARILGGLRRHGNYNLRVRADINDVIAALAREAGWVVLPDGTTFPSKSQGTKPTG-GSSAVAAGSSASHIASQQTSPPALRVVSSGLRSPVELSSCRMKGVFTPAPSPYDMLPIQSPELVGSVNKAEGLVGCS----VDVINSKQIL-EIPPNLTEQDFSGTPYV---PVYVMLPLGVINMKCELADR---------------DGLLKHLRILK-SIHVDGVKVDCWWGIVEGHSPQEYNWTGYRQLFQMVRDLNLKIQVLMSFHECGGNVGDDVCIPLPHWVAEIGRTNPDIYFTDREGRRNPECLSWGIDKERILRGRTALEVYFDYMRSFRIELAEFLEDGVISMVEIGLGPCGELRYPSCPIKHGWRYPGVGEFQCYDKYLSKSLRKAAESRGHLFWARGPDNTG-------------SYNSQPQGTGFFCDGGDYDGLYGRFFLKWYSQVLIDHADQILCLAKLVFDSSCIAAKLPDVHWWYRTASHAAELTAGFYNPSNRDGYSAIASTLKKHGATLSFVSGEVQVLNRPDDFSGALGEPEAVAWQVLNAAWDSGTPVARENSLACHDRVGYNKMLESVKFRNDPDRKHLSSFAYSRLVPALMEGHNIVEFERFVKKLHGEAVMNHHHHHHQQV-
Phaseolus_vulgaris_Phvul.001G016050.2.p         -----------------------------------------------------------------ASRRKPSWRERENNRRRERRRRAIAAKIYSGLRAQGSYNLPKHCDNNEVLKALCAEAGWCVEDDGTTYRKS-------------------------SQSPSPFSSSYPSPIPS-YQVS---------PSSS-----SFPRLDV-------------------DKDSVSNLI---------------PYIRN-------PPLRISNSAPVTPPLSSPTSRNPKPIPTW-SIAKESMASF---------NYPLFAASAPASPT------HRHLY--------------TIPEC--DES-TSTCESSQWM----------------------------------------------------KFQAFAP----SASTLPTSPTFN--KPLVPHIV------------------------------------PDN-SIQEM---------RTQVMP----------------------WVGEKI------------------------------HEVALDDLELTLGSGK-------------------------------------------------------------------------------------------------------------------------------------------
Phaseolus_vulgaris_Phvul.002G026800.2.p         -----------------------------------------------------------------STGRMPTWKERENNKRRERRRRAIAAKIYTGLRAQGNFKLPKHCDNNEVLKALCAEAGWIVEEDGTTYRKS-------------------------SIQPSPQSSSFPSPAPS-YHAS---------PTSS-----SFPPTRI-------------------DANPSSFLI---------------PFIRN-------PPLRISNSAPVTPPLSSPRTS------------------------------------------------KRKANF-----------DSTIPEC--DES--------------------------------------------------------------------------------------------------------------------------------------------------------RVKP----------------------WEGERI------------------------------HEVGMDDLELTLGFGK-------------------------------------------------------------------------------------------------------------------------------------------
Phaseolus_vulgaris_Phvul.008G065600.1.p         -----------------------------------------------------------------GTRRSRPVEEKERTKLRERRRRAITARILAGLRRHGNYNLRVRADINDVIAALAREAGWVVLPDGTTFPSE------------------------------------------------------------------------------------------------KQIA-DLPPRLPERDLAGSPYV---PVYVMLPLGVINIKCELVDP---------------DGLLKQLRVLK-SVHVDGVMVDCWWGIVEAHAPQEYTW--YKRLFQMVREVKLKLQVVMSFHECGGNFGDDVCIPLPHWVAEIGRSNPDIFFTDREGRHNPECLSWGIDKERVLRGRTAVEVYFDFMRSFRVEFDEYFEDGLISMVEVGLGPCGELRYPSCPVKHGWRYPGIGEFQCYDQYMLKSLRKAAEARGHAIWARGPDNAG-------------TYNSQPHETGFFCDGGDYDGFYGRFFLSWYSQVL-DHGNRVLSLAKLAFEGSCVTAKLSGIYWWYKTASHAAELTAGYYNPCNRDGYAAILTMLKINGVSLNIPCVELHTLNQ---------DPEGLVWQVLNAGWDVDLPVTSQNGFPCLNRVSYNKVLDHAKPMNDPDGRHFSSFTY-RLSPVLMERQNFIEFERF---------------------
'Vigna unguiculata scaffold30811-0.2'           MKS----------------------INDDGSTQDLDPQSDHSSDYLAHPNSNPQPHPHPRRPRSVAKGKKEREKEKERTKLRERHRRAITSRMLAGLRQYGNFPLPARADMNDVLAALAREAGWVVDADGTTY----------------------------RQCPPPSHMGVKETIEN--QTSVLRIDECLSPA-------SIDSVVIAERDSKNEKYTNASPINTVDCLEADQLMQDIHSGVHENDFTGTPYV---PVYVKLPAGIINKFCQLIDP---------------EGIRQELMHMK-SLNVDGVVVDCWWGIVEGWSPQKYVWSGYRELFN------------MAFHECGGNDSSDALISLPQWVLDIGKDNQDIFFTDREGRR-------GIDKERVLKGRTGIEVYFDMMRSFRTEFDDLFAEGLISAVEVGLGASGELKYPSFSERMGWR-----EFQCYDKYLQHSLRRAAKLRGHSFWARGPDNAG-------------HYNSMPHETGFFCERGDYDNYYGRFFLHWYSQTLIDHADNVLSLATLAFEETKIIVKVPAVYWWYKTPSHAAELTAGYHN-----GYSPVFEVLRKHAVTMKFVCLGFHLSSQ--EANESLIDPEGL-----------------SNALLCYDREGYKRLVDTAKPRNDPDHRHFSFFVY-QQPSLLQANVCLSDLDFFVKCMH----------------
'Vigna unguiculata scaffold56985-augustus0.2'   MTS-------------------------DGATS------------------------------AITNRRKPSWRERENNRRRERRRRAIAAKIYTGLRAQGNYNLPKHCDNNEVLKALCAEAGWTVEEDGTTYRKGCRAPLPGG-AGTS----TRNTPF--SQNPSPLSSSFPSPI-S-YQVS---------PSSS-----SFPSPS---------------------------LI---------------PYIRH-SFSASLPPLRISNSAPVTPPLSSPTSRNPKPIPTWDSIVKASMASSFNHHHHHHQNHPFFAASAPASPT------HRHLHA-----------PPTIPEC--DESDTSTVE-GQWL----------------------------------------------------NFQAFG--------------------PVCQ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
;
END;

[ The following blocks are output data for analysis step 22582 ]
BEGIN TREES;
      TITLE Cowpea_bean_BES;
      LINK TAXA = TaxaForAnalysisStep22582;
      TREE Cowpea_bean_BES = [&R] ((Arabidopsis_thaliana_AT1G19350.1:0.11085410090454037,(('Vigna unguiculata scaffold56985-augustus0.2':0.056635074813550706,Phaseolus_vulgaris_Phvul.001G016050.2.p:0.08058808122309978):0.0034723463620545897,Phaseolus_vulgaris_Phvul.002G026800.2.p:0.26932696435032166):0.2180883437610561):1.7512328332086708,(Arabidopsis_thaliana_AT2G45880.1:0.24381994448019917,Phaseolus_vulgaris_Phvul.008G065600.1.p:0.13317556584519752):0.2953677751319924,'Vigna unguiculata scaffold30811-0.2':0.35457676091219925)OROOT;
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr107973]


END;