#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 May 10, 2024; 19:42 GMT TreeBASE (cc) 1994-2008 Study reference: Egan A.N., & Doyle J. 2010. A Comparison of Global, Gene-Specific, and Relaxed Clock Methods in a Comparative Genomics Framework: Dating the Polyploid History of Soybean (Glycine max). Systematic Biology, . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S10632] BEGIN TAXA; TITLE Untitled_Taxa_Block; DIMENSIONS NTAX=10; TAXLABELS Glycine_max_OPR3_TA73832_3847 Glycine_max_PI_H1 Glycine_max_PI_H2 Glycine_max_Williams_H1 Glycine_max_Williams_H2 Glycine_tomentella_1_H1 Glycine_tomentella_2_H1 Medicago_truncatula_DY616613 Phaseolus_vulgaris_1 Phaseolus_vulgaris_2 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M5844] TITLE geneE; LINK TAXA = Untitled_Taxa_Block; DIMENSIONS NCHAR=1128; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400 410 420 430 440 450 460 470 480 490 500 510 520 530 540 550 560 570 580 590 600 610 620 630 640 650 660 670 680 690 700 710 720 730 740 750 760 770 780 790 800 810 820 830 840 850 860 870 880 890 900 910 920 930 940 950 960 970 980 990 1000 1010 1020 1030 1040 1050 1060 1070 1080 1090 1100 1110 1120 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Glycine_max_OPR3_TA73832_3847 CCTCTCCTCACCTCATACAAGATGGGAAATTTTAATCTATCCCACAGGATTGTGTTGGCACCG---ACACGATCAAGGTCTTACAACTTCGTTCCTCAGCCGCATGCTGCTCTGTATTATTCTCAAAGAACTACTAAGGGTGGCTTCTTGATCGGGGAAGCTACTGGTGTATCTGATACGGCAAAGGATGGGTAC---CCTAATACACCTGGCATTTGGACAAGAGAACAGGTGGAAGCTTGGAAACCAATTGTGAGCACTGTTCATGAGAAGGGAGGTATTTTCTTTTGTCAACTTTGGCATGCTGGGAAAGTCTCCAACTATGATGAATTCCAACCACATGGTGAAGCCCCAATATCAAGCACAAACAAGCGA---------------------------------------------------CCTCGTAAG------------GAAATCCCCAAGCTTGTCAATGAATTCGTAATTGCGGCCAAAAATGCCATGGAAGCG---------------------------------GGTTTTGATGGAATAGAACTACATGGAGCAAATGGGTACTTGCTGGATCAGTTCCTAAAGGACAAAGTGAACGACGAAGATGATGAGTACGGAGGTACTATAGAAAATCGTTGCCGGTTCCCACTGCAAGTGGTGAAGGCAGTAGCTGATGAGATCGGAGCTGACAAGGTTGGGATTAGGCTCTCCCCTTTTGCTGATTGCGTAGGA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Glycine_max_PI_H1 CCTCTTCTTACTCCTTACAGGATGGGGAACTTAAATCTTTCACACAGAATCGTTTTGGCGCCACTATTTAGAGCAAGATCTTACAACAACGTTGCTCAGCCGCATGCTATTCTATATTACTCTCAAAGAGCTACCAAGGGAGGTCTTCTGATTACTGAAGCTACTACTATTTCACCCACTTCTAAA------TACCATCCAAACGCAGTTGGTATATGGTCAAGAGAGCAAATCGAAGCATGGAAACCCATTGTGGATGCTGTTCATGCCAAAGGTGGTATATTCTTCTGTCAGATTGTTCATACTGGAAGGGCTTACGATCCAGAT---CTTAAGCCCGATGGACAAACCTTAATATCATCAACCAACAAGCCATTTACA------------CATAATGCCACCGAA------------------CCAACGGCACTAAGGACGGCTGAAATTCCTGATATCGTCAATGAATTCAGACTTGCAGCAAGGAATGCTATTGAAGCA---------------------------------GGGTTTGATGGAGTTGAGATCCATGGGGCACATGGTTTTCTAATTGATCAATTTTTGAAAGACCAAGTTAACGACAGAACAGACAAATACGGTGGATCATTGGAGAATCGTTGTCGTTTTGCATTAGAAGTTGTTGAAGCTGTTGTTGAGGAGATAGGGGCAGATAGAGTTGGAATGAGACTTTCACCCTTTTCAGACTTCAATGAATGTAGTGACTCAAATCCTCAAGCATTAGGTCTCTACATGGCCAAATCACTTAGCAAACATGGTGTGCTTTATTGCCACATGGTTGAGCCAAGATGGGACATTTCTGGGGAGAATAAGGAAACCCTTCACACTCTTTCACCAATGAAGAAAGCTTTTGATGGAACCTTCATTGTTGCTGGGGGTTATGATAGAGAAGAAGGGAACAAGGCTGTGACCGCGGACAAGGCAAATCTTGTTGCTTATGGCCGTTTGTTTTTGGCTAATCCGGATTTGCCTAAAAGGTTTGAGGTTGATGAACCACTCAACAAGTACAATAGGGATACCTTCTACACTCCTGATCCAGTTGTGGGTTATACTGACTACCCATTTCTTGAAGGTAGTGTG Glycine_max_PI_H2 CCTCTTCTTACTCCTTACGGGATGGGGAACTTCAATCTATCCCACAGAATCGTTTTGGCACCACTATTTAGAGCAAGATCTTACAACAACGTTGCTCAGCCCCATGCTATTCTATATTACTCTCAAAGAGCTACCAAGGGAGGTCTTCTAATTACTGAAGCCAATAGTATTTCACCCACTTGTCAA------TACCATCCAAACGCAGTTGGTATATGGTCAAAAGAGCAAATTGAAGCATGGAAACCCATTGTGGATGCTGTTCATGCCAAAGGTGGTATATTCTTCTGTCAGATTCTTCATACTGGAAGGGTTTCAGATCCAGAT---TTTAAGCCCAATAGACAAACCTTAATATCATCAACCAACAAGCCATTGACA------------CATAATGGCATCGAA------------------CCAAGGGCACTAAGGACAGATGAAATTCCTCATATCGTCAATGACTTCAGGCTTGCTGCAAGGAATGCTATTGAAGCA---------------------------------GGGTTTGATGGAGTTGAGATACATGGGGCACATGGTTTTCTAATTGATCAGTTTTTGAAAGATCAAGTTAACGACAGAACAGACAAATATGGTGGATCCACGGAGAACCGTTGTCGCTTTGCATTAGAAGTTGTTGAAGCTGTTGTAGAAGAAATAGGGGCAGATAGAGTTGGAATAAGACTTTCACCCTTTTCAGACTACAATGAATGTAATGACTCTAATCCTCAAGCATTGGGTCTCTACATGGCCAAATCACTTAACAAACATGGTGTGCTTTATTGTCACATGGTTGAGCCAAGATGGGACATTTCTGGGGAGAATAAGGAAACCCCTCACACTCTTGCACCAATGAAGAAGGCCTTTAATGGCACTTTCATTGTTGCTGGGGGTTATGATAGAAAAGAAGGGAACAAGGCTGTGGCTGAGGAGAAGGCAAATCTTGTTGCTTATGGTCGTTTGTTTTTGGCTAATCCAGATTTGCCTAAGAGGTTTGAGGTTGATGCACCACTCAACAAGTACAACAGGGAGACCTTCTACACTCCTGATCCAGTTGTGGGTTATACTGACTATCCATTTCTAGAAGGAAGTTCT Glycine_max_Williams_H1 CCTCTTCTTACTCCTTACAGGATGGGGAACTTAAATCTTTCACACAGAATCGTTTTGGCGCCACTATTTAGAGCAAGATCTTACAACAACGTTGCTCAGCCGCATGCTATTCTATATTACTCTCAAAGAGCTACCAAGGGAGGTCTTCTGATTACTGAAGCTACTACTATTTCACCCACTTCTAAA------TACCATCCAAACGCAGTTGGTATATGGTCAAGAGAGCAAATCGAAGCATGGAAACCCATTGTGGATGCTGTTCATGCCAAAGGTGGTATATTCTTCTGTCAGATTGTTCATACTGGAAGGGCTTACGATCCAGAT---CTTAAGCCCGATGGACAAACCTTAATATCATCAACCAACAAGCCATTTACA------------CATAATGCCACCGAA------------------CCAACGGCACTAAGGACGGCTGAAATTCCTGATATCGTCAATGAATTCAGACTTGCAGCAAGGAATGCTATTGAAGCA---------------------------------GGGTTTGATGGAGTTGAGATCCATGGGGCACATGGTTTTCTAATTGATCAATTTTTGAAAGACCAAGTTAACGACAGAACAGACAAATACGGTGGATCATTGGAGAATCGTTGTCGTTTTGCATTAGAAGTTGTTGAAGCTGTTGTTGAGGAGATAGGGGCAGATAGAGTTGGAATGAGACTTTCACCCTTTTCAGACTTCAATGAATGTAGTGACTCAAATCCTCAAGCATTAGGTCTCTACATGGCCAAATCACTTAGCAAACATGGTGTGCTTTATTGCCACATGGTTGAGCCAAGATGGGACATTTCTGGGGAGAATAAGGAAACCCTTCACACTCTTTCACCAATGAAGAAAGCTTTTGATGGAACCTTCATTGTTGCTGGGGGTTATGATAGAGAAGAAGGGAACAAGGCTGTGACCGCGGACAAGGCAAATCTTGTTGCTTATGGCCGTTTGTTTTTGGCTAATCCGGATTTGCCTAAAAGGTTTGAGGTTGATGAACCACTCAACAAGTACAATAGGGATACCTTCTACACTCCTGATCCAGTTGTGGGTTATACTGACTACCCATTTCTTGAAGGTAGTGTG Glycine_max_Williams_H2 CCTCTTCTTACTCCTTACGGGATGGGGAACTTCAATCTATCCCACAGAATCGTTTTGGCACCACTATTTAGAGCAAGATCTTACAACAACGTTGCTCAGCCCCATGCTATTCTATATTACTCTCAAAGAGCTACCAAGGGAGGTCTTCTAATTACTGAAGCCAATAGTATTTCACCCACTTGTCAA------TACCATCCAAACGCAGTTGGTATATGGTCAAAAGAGCAAATTGAAGCATGGAAACCCATTGTGGATGCTGTTCATGCCAAAGGTGGTATATTCTTCTGTCAGATTCTTCATACTGGAAGGGTTTCAGATCCAGAT---TTTAAGCCCAATAGACAAACCTTAATATCATCAACCAACAAGCCATTGACA------------CATAATGGCATCGAA------------------CCAAGGGCACTAAGGACAGATGAAATTCCTCATATCGTCAATGACTTCAGGCTTGCTGCAAGGAATGCTATTGAAGCAGATATTCAATTCCTAACCGCAATTGCAATTGTAGGGTTTGATGGAGTTGAGATACATGGGGCACATGGTTTTCTAATTGATCAGTTTTTGAAAGATCAAGTTAACGACAGAACAGACAAATATGGTGGATCCACGGAGAACCGTTGTCGCTTTGCATTAGAAGTTGTTGAAGCTGTTGTAGAAGAAATAGGGGCAGATAGAGTTGGAATAAGACTTTCACCCTTTTCAGACTACAATGAATGTAATGACTCTAATCCTCAAGCATTGGGTCTCTACATGGCCAAATCACTTAACAAACATGGTGTGCTTTATTGTCACATGGTTGAGCCAAGATGGGACATTTCTGGGGAGAATAAGGAAACCCCTCACACTCTTGCACCAATGAAGAAGGCCTTTAATGGCACTTTCATTGTTGCTGGGGGTTATGATAGAAAAGAAGGGAACAAGGCTGTGGCTGAGGAGAAGGCAAATCTTGTTGCTTATGGTCGTTTGTTTTTGGCTAATCCAGATTTGCCTAAGAGGTTTGAGGTTGATGCACCACTCAACAAGTACAATAGGGAGACCTTCTACACTCCTGATCCAGTTGTGGGTTATACTGACTATCCATTTCTAGAAGGAAGTTCT Glycine_tomentella_1_H1 CCTCTTCTTACTCCTTACAGGATGGGGAACTTCAATCTTTCACACAGAATCGTTTTGGCGCCACTATTTAGAGCAAGATCTTACAACAACGTTGCTCAGCCCCATGCTATTCTATATTACTCTCAAAGAGCTACCAAGGGAGGTCTTCTGATTGCTGAAGCTAATATTATTTCATCCACTTGTCAA------TACCATCCAAACGCAGTTGGTATATGGTCAAGAGAGCAAATCGAAGCATGGAAACCCATTGTGGATGCTGTTCATGCCAAAGGTGGTATATTCTTCTGTCAGATTGTTCATACTGGAAGGGCTTTCGATCCAGAT---TTTAAGCCCAATGGACAAGCCTTAATATCATCAACCAATAAGTCATTTACA------------CATAATGGCATGGAA------------------ACAAGGGCACTAAGGACAGATGAAATCCCTCATATAGTCAATGAATTCAGACTTGCAGCAAGGAATGCTATTGAAGCA---------------------------------GGGTTTGATGGAGTTGAGATACATGGGGCACATGGTTATCTAATTGATCAATTTTTGAAAGATCAAGTTAACGACAGAACAGACAAATATGGTGGATCATTGGAGAATCGTTGCCGTTTTGCATTAGAAGTTGTTGAAGCTGTTGTTGAAGAGATAGGGGCAGATAGAGTTGGAATGAGACTTTCACCCTTTTCAGACTACAATGAATGTAGTGACTCAAATCCTCAAGCATTAGGTCTCTACATGGCCAAATCACTTAGCAAACATGGTGTGCTTTATTGCCACATGGTTGAGCCAAGATGGGACATTTCTGGGAAGAATAAGGAAACCCTTCACACTCTTGCACCAATGAAGAAGGCTTTTGATGGAACTTTCATTGTTGCTGGGGGTTATGATAGAGAAGAAGGGAACAAGGCTGTGGCCGAGGACAAGGCAAATCTTGTTGCTTATGGTCGTTTGTTTTTGGCTAATCCGGATTTGCCTAAGAGGTTTGAGGTTGATGCACCACTCAACAAGTACAATAGGGATACCTTCTACACTCCCGATCCAGTTGTGGGTTATACTGACTACCCATTTCTTGAAGGTAGTG-- Glycine_tomentella_2_H1 CCTCTTCTTACTCCTTACAGGATGGGGAACTTCAATCTTTCACACAGAATCGCTTTGGCGCCACTATTTAGAGGAAGATCTTATAACAACGTTGCTCAGCCCCATGCCATTCTATATTACTCTCAAAGAGCTACCAAGGGAGGTCTTCTGATTGCTGAAGCTAATATTATTTCACCCACTTGTCAA------TACCATCCAAACGCAGTTGGTATATGGTCAAGAGAGCAAATCGAAGCATGGAAACCCATTGTGGATGCTGTTCATGCCAAAGGTGGTATATTCTTCTGTCAGATTATTCATACTGGAAGGGTTTACGATCCAGAT---TTTAAGCCCAATGGTCAAACCTTAATATCATCAACCAACAAGCCATTTACA------------CATAATGGCATCGAG------------------CCAAGGGCACTAAGGACAGATGAAATTCCTCATATCGTCAATGACTTCAGACTTGCAGCAAGGAATGCTATTGAAGCA---------------------------------GGTTTTGATGGAGTTGAGATCCATGGGGCACATGGTTATCTAATTGATGAATTTTTGAAAGATCAAGTTAACGACAGAACAGACAAATATGGTGGATCATTGGAGAATCGTTGCCGTTTTGCATTAGAAGTTGTTGAAGCTGTTGTTGAAGAGATAGGGGCAGATAGAGTTGGAATGAGACTTTCACCCTTTTCAGACAACTATGAATGTAGTGACTCAAATCCTCAAGCATTAGGTCTCTACATGGCCAAATCACTTAGCAAACATGGTGTGCTTTATTGCCACATGGTTGAGCCAAGATGGGACATTTCTGGGGAGAATAAGGAAACCCTTCATACTCTTGCACCAATGAAAAAGGCTTTTGATGGAACTTTCATTGTTGCTGGGGGTTATGATAGAGAAGAAGGGAACAAGGCTGTGGCCGAGGACAAGGCAAATCTTGTTGCTTATGGTCGTTTGTTTTTGGCTAATCCGGATTTGCCTAAGAGGTTTGAGGTTGATGCACCACTCAACAAGTACAATAGGGATACGTTCTACACTCCCGATCCAGTTGTGGGTTATACTGACTACCCATTTATTGAAGGTAGTG-- Medicago_truncatula_DY616613 CCTCTTCTTACTCCTTACAAAATGGGAAAATTTAATCTATCTCATAGAGTTGTTTTGGCACCATTGACTAGACAAAGATTCTACCACAATGCACCTCAACCCCATACTACTTTGTATTACTCTCAGAGGACTTCTCAAGGAGGTCTTCTCATAGCTGAATCTACTGGTGTCTCTGAAACCTCTCTA---GGGTAT---CCAAACACACCAGGCATTTGGAGAAAAGATCAAGTTGAAACTTGGAAACCCATTATTGATGCTGTTCATGCCAAAGAAGGTATATTCTTTTGTCAGATTTGGCATGGTGGAAGGGCTTCTAATTCAGGT---TATCAACCAAATGGGCAGGCACCAATATCTTCTACTAACATGTCACTCAAACCACAAACTCGAAGCAATGGCATTGATATAGCTAAGTTCACACCACCAAGGCGCCTAAGGACCTGTGAAATTCCTCGTATCGTCAATGACTTCAGACTTGCTGCAAGGAATGCTATAGCAGCT---------------------------------GGTTTTGATGGAGTTGAGATCCATGGGGCTCACGGTTACCTACTTGAGCAATTTATGAAAGATAAAGTGAATGACCGAACTGATAAATACGGCGGAAACCTTGAAAACCGTTGTCGATTCGCTTTGGAAATTGT-GAAGCTGTTGTGAATGAGATAGGTGCAGAAAGAGTTGGAATTAGATTATCGCCTTTCGCAAAATATGGAGAATGTGGAGACTCCATCT---GAAAATTGGGGCTTTTTATGGGTAATGCCTCAGTAAAACA--ATATTCTTTACTGGCACATGGGGGGACCCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Phaseolus_vulgaris_1 CCTCTTCTTACACCTCACAAAATGGGCAACTTCAATATTTCCCACAGAATCGTTTTGGCACCATTATTTAGAGCAAGATCTTACAATAATGTTCCTCAACCCCATGCTATCCTCTATTACTCCCAAAGAGCTACCAAGGGAGGTCTTCTCATTGCTGAAGCTACTAGTATTTCACCCTCTTCTAAA------TACCACTCAACCGCACCTAGTATATGGTCAAGAGAGCAAATCCAAGCATGGAAACCCGTCGTGGATGCTGTTCATGCCAAAGGTGGAATATTCTTCTGTCAGCTTGTTCATGTTGGAAGGGCTTCAGAGCAAGAT---GATGACCCAAATGGGGAACCTCTGATTTCATCAACCAACAAACCATTAAAATCT---------GGTAATGGCATGGAA------------------CCAAGGTCGTTACAGACAGATGAAATTCCTTCTATAATCAATGACTTCAGAATTGCGGCAAGGAATGCTATGGAAGCA---------------------------------GGGTTTGATGGAGTTGAGATTCATGGAGCACATGGTTTTCTGATAGAACAGTTTTTGAAAGACCAAGTTAACGACAGAAGAGACAAGTATGGTGGATCATTGGAGAATCGTTGTCGGTTTGCATTAGAAGTTGTTGAAGCTGTTGTTGAAGAAATAGGAGCAGATAGAGTTGGAATGAGACTATCACCTTTTTCAGATTACAATGAATGTAGTGATTCCAACCCTCTGGCATTGGGTCTCTACATGGCCCAATCTCTCAACAAACATGGTATTCTCTACTTGCACATGGTTGAGCCAAGATGGAACGTTGGTGGGGAGAATATGGAAAGCCCTTACACTCTTGCACCAATGAAGAAGGCCTTTAATGGCACCTTCATTGTTGCAGGGGGCTATGACAGAAAAGATGGGAACAAAGCTGTGGCTGAGAACAACACAGATCTTGTTGCTTATGGTCGTTTGTTTTTGGCTAATCCAGATTTGCCTAGAAGATTTGAGGTTGATGCACCACTCAACAAGTACAATAGGGACACCTTTTACACTCATGATCCAATTGTTGGTTACACTGACTACCCTTTTCTTGAAGCCACTGCT Phaseolus_vulgaris_2 CCTCTTCTTACACCTTACAAGATGGGCAACTTCAATATTTCCCACAGAATCGTTTTGGCACCATTATTTAGAGCAAGATCTTACAATAATGTTCCTCAGCCCCATGCTGTTCTCTATTACTCTCAAAGAGCTACCAAGGGAGGACTTCTCATTGCTGAAGCTAACAGTATTTCACCTACTTCTAAA------TATCACCCAAACGCACCTAGCATATGGTCAAGAGAGCAAATCGAAGGATGGAAACCCGTTGTGGATGCTGTTCATGCCAAAGGTGGAATATTCTTCTGTCAGCTTTTTCATGTTGGAAGGGCTTCAGAGCAAGAT---TATGATCCAAATGGGGAAGCTCCAATTTCATCAACCAACAAACCATTAAAGTCT---------GGTAATGGCATGGAA------------------CCAAGGTCGTTACAGACAGATGAAATTCCTTCTATAATCAATGACTTCAGAATTGCGGCAAGGAATGCTATGGAAGCA---------------------------------GGGTTTGATGGAGTTGAGATTCATGGAGCACATGGTTTTCTGATAGAACAGTTTTTGAAAGACCAAGTTAACGACAGAACAGACAAGTATGGTGGATCATTGGAGAATCGTTGTCGCTTTGCATTAGAAGTTGTTGAAGCTGTTGTTGAAGAAATAGGAGCAGATAGAGTTGGAATAAGACTATCACCTTTTTCAGATTACAATGAATGTAGTGATTCCAACCCTCTAGCATTGGGTCTCTACATGGCCCAATCTCTCAACAAACATGGTGTGCTCTACTTGCACATGATTGAGCCAAGATGGAACATTTCTGGGGAGACTATGGAAAGCCCTTACACTCTTGCACCAATGAAGAAGGCCTTTAATGGCACCTTCATTGTTGCAGGGGGCTATGACAGAAAAGATGGGAACAAAGCTGTGGCTGAGAACAACACAGATCTTGTTGCTTATGGTCGTTTGTTTTTGGCTAATCCAGATTTGCCTAGGAGATTTGAGGTTGATGCACCACTCAACAAGTACAATAGGGACACCTTTTACACTCATGATCCAGTTGTTGGTTACACTGACTACCCTTTTCTTGAAGCCACTGCT ; END;