#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 September 19, 2025; 10:53 GMT TreeBASE (cc) 1994-2008 Study reference: Tripathi A.K., Singh K., Pareek A., & Singla-pareek S.L. 2015. Histone chaperones in Arabidopsis and rice: genome-wide identification, phylogeny, architecture and transcriptional regulation. BMC Plant Biology, 15(42). TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S16883] [ The following blocks are input data for analysis step 15352 ] BEGIN TAXA; TITLE TaxaForAnalysisStep15352; DIMENSIONS NTAX=12; TAXLABELS Arabidopsis_thaliana_CAF1BLa Arabidopsis_thaliana_CAF1BLb Arabidopsis_thaliana_CAF1BLc Chlamydomonas_reinhardtii_Cre13.g575950.t1.2 Homo_sapiens_CAF1B Oryza_sativa_CAF1BL Physcomitrella_patens_Phpat.001G056500.1.p Physcomitrella_patens_Phpat.001G056500.2.p Picea_abies_MA_6422g0020 Saccharomyces_cerevisiae_CAF1p60 Selaginella_moellendorffii_109484 Selaginella_moellendorffii_267866 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M25499] TITLE Histone_chaperone_CAF1B_Matrix; LINK TAXA = TaxaForAnalysisStep15352; DIMENSIONS NCHAR=1146; 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 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400 410 420 430 440 450 460 470 480 490 500 510 520 530 540 550 560 570 580 590 600 610 620 630 640 650 660 670 680 690 700 710 720 730 740 750 760 770 780 790 800 810 820 830 840 850 860 870 880 890 900 910 920 930 940 950 960 970 980 990 1000 1010 1020 1030 1040 1050 1060 1070 1080 1090 1100 1110 1120 1130 1140 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Arabidopsis_thaliana_CAF1BLa --MKGGTIQISWHDGKPVLTVDFH----PISGLLATAGADYDIKLWLI-----NSGQAEKKVPSVSYQSSLTYHGCAVNTIRFSPSGELLASGADGGELFIWK---------------------LHPSETNQSWKVHKSLSF-----HRKDVLDLQWSPDDAYLISGSVDNSCIIWDVNKGSVHQILDAHCHYVQGVAWDPLAKYVASLSSDRTCRIYANK--PQTK-SKGVEKMN-YVCQHVIMKADQQR-------GDETKT-IKTHLFHDETLPSFFRRLSWSPDGSFLLIPAGSFKVSPTSEAVNATYVFSRK--------DLSRPALQLPGASKPVVVVRFCPVAFKLRGSSSE---------------EGFFKLPYRLVFAIATLNSVYIYD-TECVAPIAVLAGLHYAAITDITWSPNASYLALSSQDGYCTLVEFEDKELGEAVSISG-----------------------------------------------------------------------------------------------------------------------------------------LLLVLSLLNLPE------------------------------------------------PD----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Arabidopsis_thaliana_CAF1BLb --MKGGTIQISWHDGKPVLTVDFH----PISGLLATAGADYDIKLWLI-----NSGQAEKKVPSVSYQSSLTYHGCAVNTIRFSPSGELLASGADGGELFIWK---------------------LHPSETNQSWKVHKSLSF-----HRKDVLDLQWSPDDAYLISGSVDNSCIIWDVNKGSVHQILDAHCHYVQGVAWDPLAKYVASLSSDRTCRIYANK--PQTK-SKGVEKMN-YVCQHVIMKADQQR-------GDETKT-IKTHLFHDETLPSFFRRLSWSPDGSFLLIPAGSFKVSPTSEAVNATYVFSRK--------DLSRPALQLPGASKPVVVVRFCPVAFKLRGSSSE---------------EGFFKLPYRLVFAIATLNSVYIYD-TECVAPIAVLAGLHYAAITDITWSPNASYLALSSQDGYCTLVEFEDKELGEAVSISVG----------------------------------------------------------------------------------------------------------------------------KKPVDGEEKKHDLEKGDELMTETT------------------------------------------------PDESKKQAELEQNEESKQPLPSK----ITTDG-------------------KEKEHIMQKTDDEVMTETRHEEENQPLQSKVNTPVSN---------------------------------KPARKRITPMAIDP---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Arabidopsis_thaliana_CAF1BLc ---------------MDVLSIPFV----FLH-LVCIR--------------------------------------------------ELLASGADGGELFIWK---------------------LHPSETNQSWKVHKSLSF-----HRKDVLDLQWSPDDAYLISGSVDNSCIIWDVNKGSVHQILDAHCHYVQGVAWDPLAKYVASLSSDRTCRIYANK--PQTK-SKGVEKMN-YVCQHVIMKADQQR-------GDETKT-IKTHLFHDETLPSFFRRLSWSPDGSFLLIPAGSFKVSPTSEAVNATYVFSRK--------DLSRPALQLPGASKPVVVVRFCPVAFKLRGSSSE---------------EGFFKLPYRLVFAIATLNSVYIYD-TECVAPIAVLAGLHYAAITDITWSPNASYLALSSQDGYCTLVEFEDKELGEAVSISVG----------------------------------------------------------------------------------------------------------------------------KKPVDGEEKKHDLEKGDELMTETT------------------------------------------------PDESKKQAELEQNEESKQPLPSK----ITTDG-------------------KEKEHIMQKTDDEVMTETRHEEENQPLQSKVNTPVSN---------------------------------KPARKRITPMAIDP---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Chlamydomonas_reinhardtii_Cre13.g575950.t1.2 MPFFDKPEWIQHAGGVSIMGVDLD----PSGVRMATCGSDNRIRIWAMRP--VLSEVAEQDPAVPKQLAVLCDALTPINAIRFAPSSQLLAAGTDDSEGLVYELREGRGSAVFG----------SGESANIENWRLRIKLRG-----HASNVLDVAWAPDSRRLATCSVDNKVKVWDTTNGHCLRTLEGHVGHVKGVAWDPFDFFLASQGD-REAIVWRLE--------------------------------------DGSQVAIIREPFEKAPIVSFGLRPGWSPDGQTLALPNG------YDKGMHTVPLIKRN--------SWVPGEFCLVGHKGPVTAIRYNPHLYTPAHKPGAAPTS------------PDDEAAGSIITAGSTDKTFSIWAPCAGDEPLAVARGFFGGMVNDVAWSADGRVMVVAAYDGSVATALFADGELGKRVPQAEVEALLAQLYGDPALRAGAAGREGGGGMGLGGRGGHSGLAAAPELMALEARARAEVEREERLNSRLRADGAAAAAAGAGAVVGAGTSGAAGPAAAGAAGLRPPLGAATGLARAAMPPTAPAAARVPLAVTQNGVGSAGRGAGVGSNSPAKAGAGGARGGPAG------------------TSGRDADQPPAKRIAVQPVGSAATAMGARAGAATAATTATAPPGVAAGAGAGAGGHGAGGGSAAASPVLVPVEALHAHFSFLIHAQPGSTGEGQVELQALNTGRDARGRPAGELLCLVGGQRCWGDSVQGAVVALAGSSRLAAAATSNGDLMIYSSAGRRLFPPIRLGWPAAFLTVAPGSSLLLALLTDGSLKLWDFGAGECLLESSVAPLLLPPGAGVPGLAAAVAAAQPPVLKVTAVRITASGAPLVVLSNAHAYVHHGGLRTWVRVADDAFPASAFTTNLTSAATGELSKLQAAVAQRRHPADVMTTSALHAARPAAAARSEQAVLEHNLASAAALQSPAEWRLWLITYVRRLAADEDESRLRDLISELLGPLRWTPATHAAAAAGSSRAGGANAPAAAAAAAATSSSWEPALGSSVSGGRWAPVFLGFDKRRLLREVVLKEVARNRSYQQLVAEVLEQLKQVDAAAAAAAAVQQPHARGQADGVNAPAGDGAAAPAGAASSQPMVMG Homo_sapiens_CAF1B --MKVITCEIAWHNKEPVYSLDFQHGTAGRIHRLASAGVDTNVRIWKVEKGPDGK-------AIVEFLSNLARHTKAVNVVRFSPTGEILASGGDDAVILLWKVNDNKEPEQIAFQ------DEDEAQLNKENWTVVKTLRG-----HLEDVYDICWATDGNLMASASVDNTAIIWDVSKGQKISIFNEHKSYVQGVTWDPLGQYVATLSCDRVLRVYSIQ-------KKRVAFNVSKMLSGIGAEGEA----------------RSYRMFHDDSMKSFFRRLSFTPDGSLLLTPAGCVESG--ENVMNTTYVFSRK--------NLKRPIAHLPCPGKATLAVRCCPVYFELRPVVE--------------TGVELMSLPYRLVFAVASEDSVLLYD-TQQSFPFGYVSNIHYHTLSDISWSSDGAFLAISSTDGYCSFVTFEKDELGIPLKEKPVLNMRT-----------------------------------------------------------------------------------------------------------------------PDTAKKTKSQTHRGSSPGPRPVEGTPA---------------------------------------------SRTQDPSSPGTTPPQARQAPAPTVIRDPPSITPAVKSPLPGPSEEKTLQPSSQNTKAHPSRRVTLNTLQAWSKTTPRRINLTPLKTDTPPSSVPTSVISTPSTEEIQSETPGDAQGSPPELKRPRLDENKGGTESLDP------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Oryza_sativa_CAF1BL --MRGGTVQINWHEQQPVLTLDFH----PVSRRLATGGSDHDIKIWVI-----ASDDSDKKLPTATYHSSLSSHSSAVNVLRFSPSGENLASGADGGGIIIWK---------------------LHSTDDGEAWKVQKTLLF-----HHKDVLDLQWSQDGAFLVSASVDNSCIVWDAIKGSVQQKLEGHLHYVQGVAWDPLGQYIASLSSDRTCRIYANK--PQGK-SKNTDRMN-FVCQHTLVKAEHQN-------HDESKPPVRAHLFHDETLPSFFRRLAWSPDGSFLVLPAGLCKYS--SEVINTAYVMSRR--------DLSRPAIQLPGASKAIVAVRFCPVLFKLRGSQS----------------DCFFKLPYRVIFAVATLNSLYVYD-TESVAPILIHAGLHYAAITDIAWSSDAKYLAVSSRDCFCTIIEFENEELGLPYNLSGT-------------------------------------------------------------------------------------------------------------------------------KELDEGNTNCENMKPLKVDSMEID---------------------------------------------AGSSKAKIKASSAAVEVTPSPPV----LAQNNILMTKDVAEG----NATSENDRPSAVDNMEVDVGENKAKMEVTPVAVQVTAPPVSTKNSASS---------------------------KPTKKRITPIAIN----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Physcomitrella_patens_Phpat.001G056500.1.p --MKGATVQIAWHGSEPVLSLDFH----PHSGLLATAGADHDIKVVLHRH-IWSVHQKESGSPTVEFEADLCYHSKAVNVLRFSPSGQLLASGGDGGEILIWKP--------------------IERADKKPSWKVLKTLQL-----HVRDVLDLAWSPDSLSLMSGSVDNQCMIWDVVSGKVLQVLNDHQHFVQGVAWDPAGEFLTSISSDRTCRIYSRQSVPKSKKRKLAVVQNMFTCKQVLAKSDALPSKTNITIDADGRVAKASQLFHDETLPSFFRRLAWSPDSSFLVVPSGLHRIAHEAPSCNVSFIFSRS--------DLSRPCIHLPAPTKPVVAVRFCPVIFSLRENETE------------KGSSSGFALPYRLVFAVATLDSLYVYD-TQRSEPIVIFAGIHYAAITDIAWSADAQYVAVSSQDGYCSLLIFHGNELGTKLSSGDVPANIAKFLPE---------------------------------------------------------------------NLLGKPQESLPNSTELSQVSEPVGLMNEEQSSP----------IVICPRPLKHRRITPTALPATCSPIVQKQ---------------------------------------------IADQTSITVSDKKLQRITPIALTEDGPSSSGNCLDTETVHTPSSTQNSLSAVQAADAAETPDSSTCEASSPGAKKRLRINPIPILAGEGALNSGGNVIPRRRPTDCDQSASIAKFRSLESCLQEQGVAGPATVSTE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Physcomitrella_patens_Phpat.001G056500.2.p --MKGATVQIAWHGSEPVLSLDFH----PHSGLLATAGADHDIKVVLHRH-IWSVHQKESGSPTVEFEADLCYHSKAVNVLRFSPSGQLLASGGDGGEILIWKP--------------------IERADKKPSWKVLKTLQL-----HVRDVLDLAWSPDSLSLMSGSVDNQCMIWDVVSGKVLQVLNDHQHFVQGVAWDPAGEFLTSISSDRTCRIYSRQSVPKSKKRKLAVVQNMFTCKQVLAKSDALPSKTNITIDADGRVAKASQLFHDETLPSFFRRLAWSPDSSFLVVPSGLHRIAHEAPSCNVSFIFSRS--------DLSRPCIHLPAPTKPVVAVRFCPVIFSLRENETE------------KGSSSGFALPYRLVFAVATLDSLYVYD-TQRSEPIVIFAGIHYAAITDIAWSADAQYVAVSSQDGYCSLLIFHGNELGTKLSSGDVPANIAKFLPE---------------------------------------------------------------------NLLGKPQESLPNSTELSQVSEPVGLMNEEQSSP----------IVICPRPLKHRRITPTALPATCSPIVQKQ---------------------------------------------IADQTSITVSDKKLQRITPIALTEDGPSSSGNCLDTETVHTPSSTQNSLSAVQAADAAETPDSSTCEASSPGAKKRLRINPIPILAGEGALNSGGNVIPRRRPTDCDQSASIAKFRSLESCLQEQGVAGPATVSTE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Picea_abies_MA_6422g0020 --------------------MKFW----SLHESESKK-----------------------ENPRASYESSLSYHSSAVNVLRFSPSGEQLGSGADGGELLIWK---------------------LHYTENGNSWKVLRTLSF-----HRKDILDIQWSPDGAFLISGSVDNSCIIWDANKGAVQQILDAHLHYVQGVAWDPAGQYVASLSSDRTCRIYINK--PQTARAKNQEKLN-YVCQHVIAKAELQK-------QDDGSS-TKFHLFHDETLPSFFRRLEWSPDGSFLVVPAGIHKFSADSSASNTSYIFSRK--------DFSRPALQLPGASKPIVAVRFCPVIFTLHATRS----------------DAPFKLPYRMVFAIATLNSLYIYD-TESSSPIAIMAGLHYASITDIAWSSDAKFLAVSSQDGYCTVVEFENGDLGSPASISEIPSYVASYLPQ---------------------------------------------------------------------VTLDSTNSNGERMDVDISVVDGKDMNKESKISTVEGVKTAQAMGPKQSEAVREENLNLSNVPVLVTSISGSL---------------------------------------------SNGEKSTSSQEKQEQNLQPIADS----AAKTGPAKAETEKPSRRRITPIAVKTAQDIGQNQSEAVRAENLNLSNDPVLVASISGSLSNGQESTSIQQKQEQSVQPIADAADMTGPITAEPGKPSRRRIVPIAVEKP--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Saccharomyces_cerevisiae_CAF1p60 --MEASHLQIYWHDSQPVYSLTFQKNSAN--DKLFTAGGDNKVRIWKLNRDENGQNGGVRKIESLDFLGSLTHHEQAINVIRFNSKGDVLASAGDDGQVLLWKQEDPNTQQESVVRPFGMDAETSEADENKEKWVVWKRLRGGSGATAAAEIYDLAWSPDNRNIVVACMDNSIRLFDVGAGMLVCGQSDHGHYVQGVAWDPLNQFILSQSADRSLHVYGVI-------LSSAGVVTGLKLRSKIAKAELPC---------PGDVLRTNYLFHNETLPSFFRRCSISPCGGLVVIPSGVYKVAG-DEVANCVYVYTRSGILNSAGGVKNRPAIRIPSLKKPALMAAFSPVFYET-------------------CQKSVLKLPYKLVFAIATTNEVLVYD-TDVLEPLCVVGNIHYSPITDLAWSEDGSTLLISSTDGFCSYVSIDTETQFGSRIEPPAMHAEP-----------------------------------------------------------------------------------------------------------------------LDTDESAVAAKNQREAGG---------------------------------------------------------------------------------IVNMLPVKKIPCNS------------------------------SDSKKRRIHPTPVDL----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Selaginella_moellendorffii_109484 -MIVEKPEWLRHEG-LQIFSVDFQ----PSGQRCATAGGDHKVRIWNTRP--LMKEGE-ADRGGEKLLATLCDHFGSVNCVRWSKSGLYVASGSDGSLVLIHEKRHGTGTVEFG----------SGEPANVENWKVCASLRG-----HTADVVDLAWSPDDSMLATCSLDNTVRIWKMPGGSSVAVLTGHSSLVKGVAWDPIGSFLASQSDDKTVMIWQTS--------------------------------------DWAAVHRAEGPWRKSVGSTFFRRLSWSPCGHFIITTHG------YENPSHTAQVLERG--------DWS-GTFNFVGHNAPVVAVRFNHSMFRKQPLPPPENNGEEELLQMDPKKVPKEMVPYNVVAMGSQDRNITVWT-TANPRPVFVGKHFFTQSVVDLSWSPDGYSLFCCSLDGTVASFHFEAKELGHIVSEKEMEEFRRNRYGD-------------------SRSRQESLAESPAQLFIEATAAAKKVGN---STTIVSNGNTTSNVSNTTVVTQTNKQVASTTLRAQEHEEAGTTTTVTTPKNGTLEKDQAAAQTPVKQREYRQQDGRRRIIPEALHTEDDGGRKDRESSAEKRKLSPVDASKSEAPSKRLLGSGGSGGGGGGGGVRERNGSGASKAIEVSSMERSLGLSSTTNTTVAINVTQASQLRGPDGVLSVQVRISDEESLDGP----AVAPICLEAKPVRVQDAAAGRGETG--ETDLVCSQGGEIRWRDRFAGKVTALTGNTNFWAVGCEDGSLQVYTMAGRRALPSMVVGSAAAFMDCTRG-WELLLLTRGGTMHVWDLRQSQCLLNESLLPLTLSS-------SATSSAKESGVMRIISARFSEAGAPLVVLANGHAFLFHTKMRSWLRIADDFFPSSSFVSTWPPSGDGELAGLQKGAATLGKTNFSWNRTLINEK------YQTRAHLEDQLAAALALKSAEEYKRHLISYTRFLTREADEVRLRELCEDLLGPLFVPDS-------------------------------EPCYDSQPTTSTWESYVLGMKKRELLKNEVLPAMASNRAVQRLLNEFLDMLSEYEDTQ----------------------------------------- Selaginella_moellendorffii_267866 -MIVEKPEWLRHEG-LQIFSVDFQ----PSGQRCATAGGDHKVRIWNTRP--LMKEGE-ADRGGEKLLATLCDHFGSVNCVRWSKSGLYVASGSDGSLVLIHEKRHGTGTVEFG----------SGEPANVENWKVCASLRG-----HTADVVDLAWSPDDSMLATCSLDNTVRIWKMPGGSSVAVLTGHSSLVKGVAWDPIGSFLASQSDDKTVMIWQTS--------------------------------------DWAAVHRAEGPWRKSVGSTFFRRLSWSPCGHFIITTHG------YENPSHTAQVLERG--------DWS-GTFNFVGHNAPVVAVRFNHSMFRKQPLPPPENNGEEELLQMDPKKVPKEMVPYNVVAMGSQDRNITVWT-TANPRPVFVGKHFFTQSVVDLSWSPDGYSLFCCSLDGTVASFHFEAKELGHIVSEKEMEEFRRNRYGD-------------------SRSRQESLAESPAQLFIEATAAAKKVGN---STTIVSN------------------------------DQAAAVAVAAAPLP-----PPPAKQTPVKQREYRQQDGRRRIIPEALHTEDDDCWEAAAVA-----------------------------------------VVAELAVFVSGMAPARAKPSK------FQAWRASQLRGPDGVLSVQVRIPDEESLDGP----AVAPICLEAKPVRVQDAAAGRGETG--ETDLVCSQGGEIRWRDRFAGKVTALTGNTNFWAVGCEDGSLQVYTMAGRRALPSMVVGSAAAFMDCTRG-WELLLLTRGGTMHVWDLRQSQCLLNESLLSLTLSS-------SATSSAKENGVMRIISARFSEAGAPLVVLANGHAFLFHSKMRSWLRIADDFFPSSSFVSTWPPSGDGELAGLQKGAATLGKTNFSWNRTLINEK------YQTRAHLEDQLAAALALKSAEEYKRHLISYTRFLTREADEVRLRELCEDLLGPLFVPDS-------------------------------EPCYDSQPTTSTWESYVLGMKKRELLKNEVLPAMASNRAVQRLLNEFLDMLSEYEDTQ----------------------------------------- ; END; [ The following blocks are output data for analysis step 15352 ] BEGIN TREES; TITLE Histone_chaperone_CAF1B_Result; LINK TAXA = TaxaForAnalysisStep15352; TREE CAF1B_tree = [&R] (((((((Arabidopsis_thaliana_CAF1BLb,Arabidopsis_thaliana_CAF1BLc)0.9770,Arabidopsis_thaliana_CAF1BLa)1.0000,Oryza_sativa_CAF1BL)0.8040,Picea_abies_MA_6422g0020)0.9930,(Physcomitrella_patens_Phpat.001G056500.1.p,Physcomitrella_patens_Phpat.001G056500.2.p)1.0000)0.9980,(Homo_sapiens_CAF1B,Saccharomyces_cerevisiae_CAF1p60)0.7340)1.0000,(Chlamydomonas_reinhardtii_Cre13.g575950.t1.2,(Selaginella_moellendorffii_109484,Selaginella_moellendorffii_267866)1.0000)1.0000); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr80623] END;