#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 July 11, 2025; 19:42 GMT TreeBASE (cc) 1994-2008 Study reference: Linguiti G., Antonacci R., Tasco G., Grande F., Casadio R., Massari S., Castelli V., Consiglio A., Lefranc M., & Ciccarese S. 2016. Genomic and expression analyses of Tursiops truncatus T cell receptor gamma (TRG) and alpha/delta (TRA/TRD) loci reveal a similar basic public γδ repertoire in dolphin and human. BMC Genomics, . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S19396] [ The following blocks are input data for analysis step 18489 ] BEGIN TAXA; TITLE TaxaForAnalysisStep18489; DIMENSIONS NTAX=24; TAXLABELS Camelus_dromedarius_TRGV1_F Camelus_dromedarius_TRGV2_F Homo_sapiens_TRGV10_ORF Homo_sapiens_TRGV11_ORF Homo_sapiens_TRGV2_F Homo_sapiens_TRGV3_F Homo_sapiens_TRGV4_F Homo_sapiens_TRGV5_F Homo_sapiens_TRGV8_F Homo_sapiens_TRGV9_F Ovis_aries_TRGV1_F Ovis_aries_TRGV11_1_P Ovis_aries_TRGV2_1_F Ovis_aries_TRGV3_1_F Ovis_aries_TRGV3_2_F Ovis_aries_TRGV4_F Ovis_aries_TRGV5_1_F Ovis_aries_TRGV5_2_F Ovis_aries_TRGV6_1_F Ovis_aries_TRGV7_F Ovis_aries_TRGV8_1_F Ovis_aries_TRGV9_1_F Tursiops_truncatus_TRGV1_F Tursiops_truncatus_TRGV2_F ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M36817] TITLE Tursiops_truncatus_4A_al_Vgamma_2; LINK TAXA = TaxaForAnalysisStep18489; DIMENSIONS NCHAR=341; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" 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 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Camelus_dromedarius_TRGV1_F --------------TCTTCCA----ACATGGAA-----GGGGACAAGACGTCAGTCACAATGAAGA------TAGGATCGTCTTTTGAAATGACTTGTGATCTTAATACACAAA------GTGTCAACTATATCCACTGGTATAAATTCGGGGACAGGACAGCTCCACGACGCCTATTCTACTATGATGTCTACTACAAAATGACTTCGTACGACTCAGGAATCGATCGAAAGAAATCCCGTGCTTATGAAGGA---GCAGAGAAGAAAAATAAACTGCTCATCTCCAATCTGGAAGACAGCGATTCTGGCACGTACCGCTGTGCCATCTGG--------- Camelus_dromedarius_TRGV2_F ---------------------------GAGGTA-----AGGCTGGTGCAGCCGGCCCTGGTGATGGCGCGCACCAGGGGCTCGACTACCCTGCCCTGCCGGACCTACGGCT---------CTGTCACCTATGTCCACTGGTACCGCCAACTGGAGGGCCGGGCCCCCGAGAGGCTCCTCTATCTGGCCTTGTCGAAGAGGGATGTGCAGTGGGATTCGGTACTGAGAGGTGATAAAGTCAACGCCCAGGTGAACAACGATGGCAGAAGCTGCTTCTTGTCGCTGATGAAGCTGGAGAAGGCTGATGAGGGCACGTACTACTGTGCTGCCTGGGACGCC--- Homo_sapiens_TRGV10_ORF --------------TTATCAA----AAGTGGAG-----CAGTTCCAGCTATCCATTTCCACGGAAG------TCAAGAAAAGTATTGACATACCTTGCAAGATATCGAGCACAAGGTTTGAAACAGATGTCATTCACTGGTACCGGCAGAAACCAAATCAGGCTTTGGAGCACCTGATCTATATTGTCTCAACAAAATCCGCAGCTCGACGCAGCATGGGTAAGACAAGCAACAAAGTGGAGGCAAGAAAGAATTCTCAAACTCTCACTTCAATCCTTACCATCAAGTCCGTAGAGAAAGAAGACATGGCCGTTTACTACTGTGCTGCGTGGTGGGTGGC- Homo_sapiens_TRGV11_ORF --------------CTTGGGC----AGTTGGAA-----CAACCTGAAATATCTATTTCCAGACCAG------CAAATAAGAGTGCCCACATATCTTGGAAGGCATCCATCCAAGGCTTTAGCAGTAAAATCATACACTGGTACTGGCAGAAACCAAACAAAGGCTTAGAATATTTATTACAT---GTCTTCTTGACAATCTCTGCTCAAGATTGCTCAGGTGGGAAGACTAAGAAACTTGAGGTAAGTAAAAATGCTCACACTTCCACTTCCACTTTGAAAATAAAGTTCTTAGAGAAAGAAGATGAGGTGGTGTACCACTGTGCCTGCTGGATTAGGCAC Homo_sapiens_TRGV2_F --------------TCTTCCA----ACTTGGAA-----GGGAGAACGAAGTCAGTCATCAGGCAGA------CTGGGTCATCTGCTGAAATCACTTGTGATCTTGCTGAAGGAA------GTAACGGCTACATCCACTGGTACCTACACCAGGAGGGGAAGGCCCCACAGCGTCTTCAGTACTATGACTCCTACAACTCCAAGGTTGTGTTGGAATCAGGAGTCAGTCCAGGGAAGTATTATACTTACGCAAGC---ACAAGGAACAACTTGAGATTGATACTGCGAAATCTAATTGAAAATGACTCTGGGGTCTATTACTGTGCCACCTGGGACGGG--- Homo_sapiens_TRGV3_F --------------TCTTCCA----ACTTGGAA-----GGGAGAACGAAGTCAGTCACCAGGCAGA------CTGGGTCATCTGCTGAAATCACTTGCGATCTTACTGTAACAA------ATACCTTCTACATCCACTGGTACCTACACCAGGAGGGGAAGGCCCCACAGCGTCTTCTGTACTATGACGTCTCCACCGCAAGGGATGTGTTGGAATCAGGACTCAGTCCAGGAAAGTATTATACTCATACACCC---AGGAGGTGGAGCTGGATATTGAGACTGCAAAATCTAATTGAAAATGATTCTGGGGTCTATTACTGTGCCACCTGGGACAGG--- Homo_sapiens_TRGV4_F --------------TCTTCCA----ACTTGGAA-----GGGAGAACGAAGTCAGTCATCAGGCAGA------CTGGGTCATCTGCTGAAATCACTTGTGATCTTGCTGAAGGAA------GTACCGGCTACATCCACTGGTACCTACACCAGGAGGGGAAGGCCCCACAGCGTCTTCTGTACTATGACTCCTACACCTCCAGCGTTGTGTTGGAATCAGGAATCAGCCCAGGGAAGTATGATACTTATGGAAGC---ACAAGGAAGAACTTGAGAATGATACTGCGAAATCTTATTGAAAATGACTCTGGAGTCTATTACTGTGCCACCTGGGATGGG--- Homo_sapiens_TRGV5_F --------------TCTTCCA----ACTTGGAA-----GGGGGAACGAAGTCAGTCACGAGGCCGA------CTAGGTCATCTGCTGAAATCACTTGTGACCTTACTGTAATAA------ATGCCTTCTACATCCACTGGTACCTACACCAGGAGGGGAAGGCCCCACAGCGTCTTCTGTACTATGACGTCTCCAACTCAAAGGATGTGTTGGAATCAGGACTCAGTCCAGGAAAGTATTATACTCATACACCC---AGGAGGTGGAGCTGGATATTGATACTACGAAATCTAATTGAAAATGATTCTGGGGTCTATTACTGTGCCACCTGGGACAGG--- Homo_sapiens_TRGV8_F --------------TCTTCCA----ACTTGGAA-----GGGAGAACAAAGTCAGTCACCAGGCCAA------CTGGGTCATCAGCTGTAATCACTTGTGATCTTCCTGTAGAAA------ATGCCGTCTACACCCACTGGTACCTACACCAGGAGGGGAAGGCCCCACAGCGTCTTCTGTACTATGACTCCTACAACTCCAGGGTTGTGTTGGAATCAGGAATCAGTCGAGAAAAGTATCATACTTATGCAAGC---ACAGGGAAGAGCCTTAAATTTATACTGGAAAATCTAATTGAACGTGACTCTGGGGTCTATTACTGTGCCACCTGGGATAGG--- Homo_sapiens_TRGV9_F --------------GCAGGTC----ACCTAGAG-----CAACCTCAAATTTCCAGTACTAAAACGC------TGTCAAAAACAGCCCGCCTGGAATGTGTGGTGTCTGGAATAACAATTTCTGCAACATCTGTATATTGGTATCGAGAGAGACCTGGTGAAGTCATACAGTTCCTGGTGTCC---ATTTCATATGACGGCACTGTCAGAAAGGAATCCGGCATTCCGTCAGGCAAATTTGAGGTGGATAGGATACCTGAAACGTCTACATCCACTCTCACCATTCACAATGTAGAGAAACAGGACATAGCTACCTACTACTGTGCCTTGTGGGAGGTG--- Ovis_aries_TRGV1_F --GTCACTCAGGTATCTTCCA----ACGCAAAA-----GGGGCCCAGATGTCAGTCACTGCTAAGA------CTTGGGACACTACTTCTTTCACTTGTGATTT---TACACAAG------ATGTCAAATATATCCACCTGTACAAACAACAGGAGGGGATGGCTCCCCGACGTCTTTTCTACTACGATGTCTACTACTCCAAGATTGAGTTCGAATCAGGAATCGATAAAGCAAAATACAGTGTTTATAAAGGTGCAGCAGGAAGGAGCTACAGATTTGCAATCCTAAATCTGGAACACAGTGATTCTGGGACGTACTACTGTGCTGTCTGGGATAAG--- Ovis_aries_TRGV11_1_P ---TTGTGTGTGTATTGTACAGGTCATCTAGAG-----CAACCTCAAATTTCCAGTACCAAAAAGC--------TGTCTAACAGCCCGCCTGGAATGT--------------AACAATTTTTACCACATCTGTATATTGGTGTCAAGAAAGACCTGGTTAAGCCATGCAGCACCTGCTACAC---ATTTTCTCTAACACC---GTCAAAAGGGAAGCAGGCATTCTGTTGAGCAAGTTTGAGGCAGACAGGATACCTGAAACTTCTACATCGACCCTCACTGTTCACAATGCACGGGGACGAGACTCTGCCACCTATTACTGTGCCCTCTGGGATGTG--- Ovis_aries_TRGV2_1_F --GTCATGCAGGTGTCTTCCA----ACATGGAA-----GGGGAGAAGATGTCAATTACTAAGGCAGCTGTGCCTGGGGCATTTGTTGAAATCATTTGTGATCTTATCACCCAAA------CCGTCAAATATATCCACTGGTACAAGCACCAGGAGGGCACAGCTCCCCGACGCCTTCTTTACTACGACATCTCCTACTCAAAGATTGTGTTGGAATCAGGAATCAGTGAAGGGAAGTACAAAGTTTATAAAGA---------GAAGAGCTATACTTTTGCAATCTCAAACCTGCAAGAAAGTGATTCTGGAATGTACTACTGTGCTGTCTGGGAGAAG--- Ovis_aries_TRGV3_1_F ------------GGTTATCAA----AAGTGGAG-----CAGGCCCAAATCTCCCTTTCCACAGAAG------TAAAGAAAAGTATTGACATACATTGCAAGATAGAGAGCACAGATTTTGAATCAGAAGCTGTTTACTGGTACCGGCAGAAAAGGAATCAGGCTTTGGAGCATCTGGTTTAT---GTGATCTCAACCACAACTGCAGCTCGAAATCAAGTAGACGGGAAGAACAAAATTGAGGCAAGAAAAGACGCTCGAATGTTCACTTCGACCCTTACGGTAAATTTTGTAGAAAAAGAAGATGTGGGCATTTACTACTGTGCTGGCTGGAGCT----- Ovis_aries_TRGV3_2_F --TCTGGACTTGGGTTATCAA----AAGTGGAG-----CAGGCCCAAATCTCCCTTTCCACAGAAG------TAAAGAAAAGTATTGACATACATTGCAAGATAGAGAGCACAGATTTCGAATCAGAAACTGTTTACTGGTACCGGCAGAAAAGGAATCAGGCTTTGGAGCATCTGGTTTAT---GTGATCTCAACCACAACTGCAGCTCGAAATCAAGTAGACGGGAAGAACAAAATTGAGGCAAGAAAAGATGCTCAAATGTTCGCTTCGACCCTTATGGTAAATTTTGTAGAAAAAGAAGATGTGGGCATTTACTACTGTGCTGGCTGGG-------- Ovis_aries_TRGV4_F ----------GGAGACATCAA----AATGAGAATTTCTCAGAATCAACTCTCCTCTACCCGAAGAC------CAGACAGAACAGTGCACATAAGTTGCAAGCTGTCAGGGGTTCCCCTGGAGAATGCCATTGTGCACTGGTATCAAGAGAAAGAAGGGGAGCCCCTGAAACGAATCCTTTAT---GGCTCAGCTAACAGTTATAAGCTGGACAAACCTAATTCCCGTTTGGAGATGGATAACAAAAAGAATGGA------------ATCTTTTACCTGATAATCAATAACGTTGTCAAGTCCGATGAAGCCACTTACTACTGTGCCTGCTGGGATCT---- Ovis_aries_TRGV5_1_F --GTCATGCAGGTATCTTCCA----ACTT-----------------GATGTTAATCACTAGAAAGA------CTGGGGAGACTGCTTCGTTCCCTTGTGATCT---TACACACG------GGGCTATCTATATCCACTTGTACAAACATGAGGAGGGGATGGCCCCCCGACGCCTTTTATACTATGACAGCTACAACTCAAAGCCTGTGTTTGAATCAGGAATCAGTGGAACAAAATACCATGTCTATAAGGGC---ACAGGGAGTAGCTATACATTTACAATCGTAAATCTGCAAGCAAGTGATTCCGGCATATACTACTGTGCTATCTGGGATAAG--- Ovis_aries_TRGV5_2_F ------------AATCTTCCA----ACTT-----------------GATGTTAATCACTAGAAAGA------CTGGGGAGACTGCTTCGTTCCCTTGTGATCT---TACACAAG------GGGCCACCTATATCCACTTGTACAAACATGAGGAGGGGATGGCCCCCCGACGCCTTTTATACTATGACAGCTACAACTCAAAGCCTGTGTTTGAATCAGGAATCAGTGGAACAAAATACCATGTCTATAAGGGC---ACAGGGAGGAGCTATACATTTGCAATCCTGAATCTGCAAGCAAGTGATTCCGGCATATACTACTGTGCTATCTGGGATAAG--- Ovis_aries_TRGV6_1_F --------------GTATCCA----GCAGGAGATCAGGCTGTCACAGCGGTCCGTGATGGTGGGGTCCG---CGGGTGGAGCTATGACTATGCCTTGCAGTGTCAGTAAGT---------CTGTGGATTACGTCCACTGGTTCCGCCAGCTGGAGGGCCAGGCCCCTGAGAGGCTTCTCTATCTAGCCTTGTCCAAGCGGGATGTGCAGTGGGATTCAGTCCTAGGAGGTGATAAAGTCAGCGCAGCCCGCGGCGGGGATGGCAAGAGCTGCACCATGTCCTTGAGGAAGCTGGCGAAGAGCGACGAGGGACTGTACTACTGTGCTGCCTGGGGATCGG-- Ovis_aries_TRGV7_F --TTTGGCCTTGGGCAATTAA----CTTTGGAG-----CAACCTGAATTATCAGTTACTGGAACAA------GAGAAAAGAGTATAATTATGACTTGCAAGGTGTTCTCTAAGGACTTTAGCAAAGATTACATCCACTGGTACCGGCAAAAACCTGATCAGGGTTTAGAACAGCTACTATAT------GTCTCAACAGCCCCTGCGCAGAATCACTTAGGAGGGAAGAAAAACAAGCTTGAGGCCAGAAAAGATGCTCCCTCTTCCACTTCTACCTTGAAAATAAGTTTTTTAGAGAAAGAAGATGAGGCTACATACTACTGTGCCGGCTGGTTGAGCGCC Ovis_aries_TRGV8_1_F -----ACACAGGTATCTTCCA----ACATGGGA-----GAGGACAAGTTGTCAGTCACGAGGGCGA------CTGGGTCATCTGTTGTAATCGATTGTGATCT---TACACAAA------------ACTATATCCACTGGTACAAATTCCAGGAGGGAACTGTGCCCCGACGCCTTCTCTACTACGATGTCTACTACTCAAAGGTTGTATTGGACTCAGGAATCAGTGAAGGGAAATACCACGTTTACAAAGGC---ACAGGGAAGAGCTACACGTTCGTAATCTCAAACTTGCAAGAAAGTGATTCTGGCACGTACTACTGTGCTGTCTGGGAGAAG--- Ovis_aries_TRGV9_1_F --GTCACTCAGGTATCTTCCA----ACATGGAA-----GGCGACAGGATGTCAATCACCAGGGCAG------CTGGGTCCTCTGCTGTAATCCCTTGTGATCTTCCTACACAAA------ACATCAAATATATCCACTGGTACAAATTCCAGGAGGGAATA---CCCCGACGCCTTCTCTACTATGATGTCTCCTACTCAAAGGTTGTGTTGGAATCAGGAATCAGTCCAGGGAAATACCACTGCTATGAAGGC---ACAGACAAGATATATAAATTTGTAATCTCAAGTCTTCAAGAAAGTGATTCTGGAGTGTACCACTGTGCTGTCTGGGAGAAG--- Tursiops_truncatus_TRGV1_F TATGTGTGTATGGTGCAGGTC----ATCTAGAG-----CAACCTCAACTCTCCACTACCAAAAAGC------TGTCAAAAACAGCCCGCCTGGAATGCGTGGTATCTGGTGTAACCATTTCTAAAATGTCTGTATATTGGTATCAAGAAAGACCTGGCGAAGCCATGCAGCACCTGCTACAC---ATTTTACCTAACAACACCGTCAGAAGGGACTCAGACGTTACACTGGGCAAGTTTGAGGCAGACAAGAAACCCGAAACTTCTACGTCGACCCTCACCATTCACAATGTACAGGAACAAGACGCGGCCACCTACTATTGTGCCCTCTGGGAAGTG--- Tursiops_truncatus_TRGV2_F ---TTGGCCTTGGGCAATTAA----AGTCGGAG-----CAACCTGTAATATCAGTTACTGGAGTAA------GAGATAAGAGTGTAGTTATATCTTGCAAGGTATCCTCTCAAGACTTTAGCAACGAATACATCCACTGGTACCGGCATAAACCAAATCAGGGTATAGAACATCTAGCATAC------GTCGTAACAGTCCCTGCTCTAAAAGACTTAGGAGGGAAGAAAAACAAGATTGAGGCCAGAAAAGACGTCCGCACCTCCACTTCTACCTTGAACATAAGATTCTTACAGAAAGAAGATGAGGCCACGTACTACTGTGCCTGGTGGGTTTA---- ; END; [ The following blocks are output data for analysis step 18489 ] BEGIN TREES; TITLE Tursiops_truncatus_4A_tr_Vgamma2; LINK TAXA = TaxaForAnalysisStep18489; TREE '4A_tr_Vgamma2' = [&R] (((((((Ovis_aries_TRGV2_1_F:0.08496,Ovis_aries_TRGV8_1_F:0.07363)0.44:0.00309,Ovis_aries_TRGV9_1_F:0.08061)0.96:0.03614,Camelus_dromedarius_TRGV1_F:0.17862)0.42:0.00458,(Ovis_aries_TRGV1_F:0.10825,(Ovis_aries_TRGV5_1_F:0.00761,Ovis_aries_TRGV5_2_F:0.01001)1.00:0.0966)0.97:0.03865)0.93:0.03427,((Homo_sapiens_TRGV3_F:0.02324,Homo_sapiens_TRGV5_F:0.0164)1.00:0.04143,(Homo_sapiens_TRGV8_F:0.05589,(Homo_sapiens_TRGV2_F:0.02067,Homo_sapiens_TRGV4_F:0.02338)1.00:0.03442)0.52:0.00813)1.00:0.09526)1.00:0.08042,(Ovis_aries_TRGV6_1_F:0.12982,Camelus_dromedarius_TRGV2_F:0.13009)1.00:0.11925)0.99:0.01753,(Ovis_aries_TRGV4_F:0.26209,(((Ovis_aries_TRGV11_1_P:0.08978,Tursiops_truncatus_TRGV1_F:0.08202)0.94:0.02539,Homo_sapiens_TRGV9_F:0.12219)1.00:0.13758,(((Ovis_aries_TRGV3_1_F:0.00431,Ovis_aries_TRGV3_2_F:0.00891)1.00:0.12849,Homo_sapiens_TRGV10_ORF:0.14905)0.98:0.04947,(Homo_sapiens_TRGV11_ORF:0.16206,(Ovis_aries_TRGV7_F:0.07066,Tursiops_truncatus_TRGV2_F:0.08353)0.99:0.04719)0.91:0.03203)1.00:0.0747)0.53:0.0087)0.99:0.03351); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr96523] END;