#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; 19:47 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 18493 ] BEGIN TAXA; TITLE TaxaForAnalysisStep18493; DIMENSIONS NTAX=24; TAXLABELS Camelus_dromedarius_TRGJ1_1_F Camelus_dromedarius_TRGJ2_1_ORF Camelus_dromedarius_TRGJ2_2_F Homo_sapiens_TRGJ1_F Homo_sapiens_TRGJ2_F Homo_sapiens_TRGJP_F Homo_sapiens_TRGJP1_F Homo_sapiens_TRGJP2_F Ovis_aries_TRGJ1_1_F Ovis_aries_TRGJ1_2_F Ovis_aries_TRGJ2_1_F Ovis_aries_TRGJ2_2_F Ovis_aries_TRGJ3_1_F Ovis_aries_TRGJ3_2_P Ovis_aries_TRGJ4_1_P Ovis_aries_TRGJ4_2_F Ovis_aries_TRGJ5_1_F Ovis_aries_TRGJ5_2_P Ovis_aries_TRGJ5_3_F Ovis_aries_TRGJ6_1_F Ovis_aries_TRGJ6_2_F Tursiops_truncatus_TRGJ1_F Tursiops_truncatus_TRGJ2_F Tursiops_truncatus_TRGJ3_F ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M36815] TITLE Tursiops_truncatus_15_al_J2; LINK TAXA = TaxaForAnalysisStep18493; DIMENSIONS NCHAR=72; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 ] [ . . . . . . . ] Camelus_dromedarius_TRGJ1_1_F ------ATAGCTCGGGC--TGGAGGAAGACATTTGGAAAAGGGACTGAGCTCATAGT----AGTTCCCCTTG Camelus_dromedarius_TRGJ2_1_ORF -GGGCTGCAAAAGGGGC--TGGAGGAAGATATTTGGAGAAGGGACTGAGCTCATAGTGACCGACCGCCCCTG Camelus_dromedarius_TRGJ2_2_F ------------GAATTA-TATAATAAAATCTTCGGTGGTGGAACAAAACTCGTAGT----------CACAG Homo_sapiens_TRGJ1_F ------------GAATTATTATAAGAAACTCTTTGGCAGTGGAACAACACTGGTTGT----------CACAG Homo_sapiens_TRGJ2_F ------------GAATTATTATAAGAAACTCTTTGGCAGTGGAACAACACTTGTTGT----------CACAG Homo_sapiens_TRGJP_F TGGGCAAGAGTTGGGCAAAAAAATCAAGGTATTTGGTCCCGGAACAAAGCTTATCAT----------TACAG Homo_sapiens_TRGJP1_F ------ATACCACTGGT--TGGTTCAAGATATTTGCTGAAGGGACTAAGCTCATAGT----AACTTCACCTG Homo_sapiens_TRGJP2_F ------ATAGTAGTGAT--TGGATCAAGACGTTTGCAAAAGGGACTAGGCTCATAGT----AACTTCGCCTG Ovis_aries_TRGJ1_1_F ------ACAGCGAGGGC--TGGAAGAAGATATTTGGAGAAGGAGCTAACATCATAAT----AACTCCTCCCG Ovis_aries_TRGJ1_2_F ------------GAATGATTACATAAAAAACTTCAATGTTGGGGCAAAACTCATTGT----------CACAG Ovis_aries_TRGJ2_1_F ------ACAGCTCGGGC--TGGAAGAAGATATTTGGAGAAGGAGCTAACATCATAGT----AACTCCTCCCG Ovis_aries_TRGJ2_2_F ------------GAATAATTACATAAAAAACTTCAATGTTGGAGCAAAACTCATTGT----------CACAG Ovis_aries_TRGJ3_1_F ------ACAGTTCAGGC--TGGAAGAAGATATTTGGAAAAGCAACTGAGCTCATAGT----AGCTTCCCCTG Ovis_aries_TRGJ3_2_P ------------AAATTATTATAGAAAAATGTTTGTTAATGGAATAAAATTT-TTGT----------CATAG Ovis_aries_TRGJ4_1_P ------ATGGCTCAGAA--TGAAAGAAGATATTTGGAAAAGGACCTAAGCTCATAAT----AGCTCCCCATG Ovis_aries_TRGJ4_2_F ------------TAATAGTTACATAAAAAACTTCAACGTTGGAACAAAACTTGTCGT----------CACAG Ovis_aries_TRGJ5_1_F -----AATCATTGTGACAAGGGATCAAGGTATTTGGTGAAGGAACTAAGCTCGTAGT--------------A Ovis_aries_TRGJ5_2_P --TGCAAACAGGTGGCCAGAGCATCGAAGTGTTTGGTTCCAGAACACAACTTATTGT----------TACAG Ovis_aries_TRGJ5_3_F ------------GAGTTATTATGTAAAAATCTTCGGCGATGGGACAAAACTTGTAGT----------CACAG Ovis_aries_TRGJ6_1_F ------ACAGCTCAGGT--TGG---AAGATGTTTGGAGAAGGAACTAAGCTCATAGT----AGCTCCCTGTG Ovis_aries_TRGJ6_2_F ------------GAATTTAAACTACATGATCTTTGGTGGAGGAACAAAAGTTTTCGT-----------CCAA Tursiops_truncatus_TRGJ1_F ------ATAGGTCAGGT--TGGATCAAGATATTTGGAGGAGGAACTAAGCTCATAGT----AACTCTCCCTG Tursiops_truncatus_TRGJ2_F --GGCTAACACATGGCAAGAGCGTCAAAGTGTTTGGTTCTGGAACACAGCTCATTGT----------TACAG Tursiops_truncatus_TRGJ3_F ------------GAGTTATTACATAAAAATTTTCGGCGATGGGACAAAACTTGTGGT----------CACAG ; END; [ The following blocks are output data for analysis step 18493 ] BEGIN TREES; TITLE Tursiops_truncatus_15_tr_J2; LINK TAXA = TaxaForAnalysisStep18493; TREE '15_tr_J2' = [&R] (((((((((Camelus_dromedarius_TRGJ2_1_ORF:0.03121,Camelus_dromedarius_TRGJ1_1_F:0.04379)0.43:0.02085,Ovis_aries_TRGJ3_1_F:0.05415)0.35:0.02533,(Ovis_aries_TRGJ1_1_F:0.04184,Ovis_aries_TRGJ2_1_F:0.00816)0.93:0.08405)0.21:0.00652,Ovis_aries_TRGJ4_1_P:0.1138)0.10:0.00737,(Ovis_aries_TRGJ6_1_F:0.02305,Tursiops_truncatus_TRGJ1_F:0.02695)0.74:0.0264)0.14:0.01648,(Homo_sapiens_TRGJP2_F:0.12536,Homo_sapiens_TRGJP1_F:0.04964)0.41:0.0311)0.55:0.0316,Ovis_aries_TRGJ5_1_F:0.09971)0.89:0.0897,(Homo_sapiens_TRGJP_F:0.12743,(Tursiops_truncatus_TRGJ2_F:0.0426,Ovis_aries_TRGJ5_2_P:0.1074)0.94:0.09757)0.81:0.06157)0.80:0.01204,(Ovis_aries_TRGJ6_2_F:0.17075,((Ovis_aries_TRGJ5_3_F:0.02639,Tursiops_truncatus_TRGJ3_F:0.04861)0.84:0.05416,(((Homo_sapiens_TRGJ1_F:0.01667,Homo_sapiens_TRGJ2_F:0.00833)1.00:0.1011,Ovis_aries_TRGJ3_2_P:0.1239)0.53:0.02677,(Camelus_dromedarius_TRGJ2_2_F:0.05703,(Ovis_aries_TRGJ4_2_F:0.075,(Ovis_aries_TRGJ1_2_F:0.03295,Ovis_aries_TRGJ2_2_F:0.01705)0.92:0.05)0.94:0.09922)0.22:0.01542)0.17:0.00912)0.50:0.03238)0.80:0.0507); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr96521] END;