#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; 21:38 GMT TreeBASE (cc) 1994-2008 Study reference: Syring J., Castillo R., Cronn R., & Liston A. 2006. Multiple nuclear loci reveal the distinctiveness of the threatened, neotropical Pinus chiapensis (Pinaceae). Systematic Botany, null. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S1631] [ The following blocks are input data for analysis step 3198 ] BEGIN TAXA; TITLE TaxaForAnalysisStep3198; DIMENSIONS NTAX=26; TAXLABELS Pinus_ayacahuite_04S2_03S3 Pinus_ayacahuite_09S2_12S1_15S2 Pinus_ayacahuite_18S2 Pinus_ayacahuite_VAR_VEITCII_01S1 Pinus_ayacahuite_VAR_VEITCII_03S2 Pinus_chiapensis_01S1 Pinus_chiapensis_01S2 Pinus_chiapensis_02S1 Pinus_chiapensis_05N Pinus_chiapensis_35S1 Pinus_chiapensis_38S1 Pinus_chiapensis_39S1 Pinus_chiapensis_41S1 Pinus_gerardiana Pinus_monticola_01S1_02S3 Pinus_monticola_02S1_07S1_05S1 Pinus_monticola_04S1 Pinus_monticola_06S1 Pinus_monticola_13S1 Pinus_monticola_16S1 Pinus_squamata Pinus_strobus_01S1 Pinus_strobus_02S1_10S1 Pinus_strobus_03S1_22S3_26Nh_09S1_05S1 Pinus_strobus_04S1 Pinus_strobus_11S2 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2673] TITLE AGP6; LINK TAXA = TaxaForAnalysisStep3198; DIMENSIONS NCHAR=779; 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 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Pinus_ayacahuite_04S2_03S3 ATGGCTCTGCATTGCAAGTTTCAGTAATGGAGAAAAGCCTCTGGTTGATACTGTGTTAGCTACTGCACCGGCGGCGCCCACCACTGCTAAACCACCCACAACTGCACCGGCGGCACCGGTCTCAACTCCGAAGCCTCCCACGACAACGCCCGTAGCGCCCGCCGTCGCTCCCACGAAACCGACTCCGCCCGTAGCGCCCGCCGTTGCTCCCACCAAGCCGGCTCCACCCGT???????????????????????????????????????CACGGCGCCCACCAAAGCTCCTCCTCCCACCACTAAACCTCCCGCCGTTGCTCCCGCCAAAGCTCCGGTTTCCGCACCGCCGGTGGCTACGCCTCCGGTTGCCGTACCCCCGGTGGCTACTCCGCCTGTCGCCGCTCCGCCAGTAGCGGTGCCTCCGGCCTCTCCTCCGGCTATTCCGCCACCGGTGCAGGCGCCGGCACCTTCGCATCACAAACGCAAGAAGAAGAAGAAG???CACCACCACCACG???CCGCCCCTGCGCCAACTCCGTCCGCACTGAAAAGCCCGCCTAGTCCTCCACTTGGGAGCCCCGGGCCTTCTACCTCGGCCGATTCCTTCGCTCCCGCCCCTTCACAACCGGTAATCTCCGCCACCATTTATTTTATTAAATCGACTTAATGGCTGTTCAGGATCTAACCGTGGCTGCCTGTTTTTGTTTTTCTTGTTTGCAGAGTGCGGGAATGAAGAGCTCCGCCGCGAGCGTGTGTGGCACGCTGGTCATCCCACA Pinus_ayacahuite_09S2_12S1_15S2 ATGGCTCTGCATTGCAAGTTTCAGTAATGGAGAAAAGCCTCTGGTTGATACTGTGTTAGCTACTGCACCGGCGGCGCCCACCACTGCTAAACCACCCACAACTGCACCGGCGGCACCGGTCTCAACTCCGAAGCCTCCCACGACAACGCCCGTAGCGCCCGCCGTCGCTCCCACGAAACCGACTCCGCCCGTAGCGCCCGCCGTTGCTCCCACCAAGCCGGCTCCACCCGT???????????????????????????????????????CACGGCGCCCACCAAAGCTCCTCCTCCCACCACTAAACCTCCCGCCGTTGCTCCCGCCAAAGCTCCGGTTTCCGCACCGCCGGTGGCTACGCCTCCGGTTGCCGTACCCCCGGTGGCTACTCCGCCTGTCGCCGCTCCGCCAGTAGCGGTGCCTCCGGCCTCTCCTCCGGCTATTCCGCCACCGGTGCAGGCGCCGGCACCTTCGCATCACAAACGCAAGAAGAAGAAGAAG???CACCACCACCACG???CCGCCCCTGCGCCAACTCCGTCCGCACTGAAAAGCCCGCCTAGTCCTCCACTTGGGAGCCCCGGGCCTTCTACCTCGGCCGATTCCTTCGCTCCCGCCCCTTCACAACCGGTAATCTCCGCCACCATTTATTTTATTAAATCGACTTAATGGCTGTTCAGGATCTGACCGTGGCTGCCTGTTTTTGTTTTTCTTGTTTGCAGAGTGCGGGAATGAAGAGCTCCGCCGCGAGCGTGTGTGGCACGCTGGTCATCCCACA Pinus_ayacahuite_18S2 ATGGCTCTGCATTGCAAGTTTCAGTAATGGAGAAGAGCCTCTGGTTGATACTGTGTTAGCTACTGCACCGGCGGCGCCCACCACTGCTAAACCACCCACAACTGCACCGGCGGCACCGGTCTCAACTCCGAAGCCTCCCACGACAACGCCCGTAGCGCCCGCCGTCGCTCCCACGAAACCGGCTCCGCCCGTAGCACCCGCCGTTGCTCCCACCAAGCCGGCTCCGCCCGT???????????????????????????????????????GACGGCGCCCACCAAAGCCCCTCCTCCCACCACTAAACCTCCCGCCGTTGCTCCCGCCAAAGCTCCGGTTTCCGCACCGCCGGTGGCTACACCTCCGGTTGCCGTACCCCCAGTGGCTACGCCGCCTGTCGCCGCTCCGCCGGTAGCGGTGCCTCCGGCCTCTCCTCCGGCTATTCCGCCACCGGTGCAAGCGCCGGCACCTTCGCATCACAAACGCAAGAAGAAGAAGAAGAAGCACCACCACCACGGCCCCGCCCCTGCGCCGACTCCGTCCGCACTGAAAAGCCCGCCCAGTCCTCCACTTGGGAGCCCCGGGCCTTCTACCTCGGCCGATTCCTTCGCTCCCGCCCCTTCACAACCGGTAATCTCCGCCACCATTTATTTTATTAAATCGACTTAATGGCTGTTCAGGATCTGACCGTGGCTGCCTGTTTTTGTTTTTCTTTTTCGCAGAGTGCGGGAATGAAGAGCTCCGCCGCGAGCGTGTGTGGCACGCTGGTCATCCAAAA Pinus_ayacahuite_VAR_VEITCII_01S1 ATGGCTCTGCATTGCAAGTTTCAGTAATGGAGAAAAGCCTCTGGTTGATACTGTGTTAGCTACTGCACCGGCGGCGCCCACCACTGCTAAACCACCCACAACTGCACCGGCGGCACCGGTCTCAACTCCGAAGCCTCCCACGACAACGCCCGTAGCGCCCGCCGTCGCTCCCACGAAACCGACTCCGCCCGTAGCGCCCGCCGTTGCTCCCACCAAGCCGGCTCCACCCGT???????????????????????????????????????CACGGCGCCCACCAAAGCTCCTCCTCCCACCACTAACCCTCCCGCCGTTGCTCCCGCCAAAGCTCCGGTTTCCGCACCGCCGGTGGCTACGCCTCCGGTTGCCGTACCCCCGGTGGCTACTCCGCCTGTCGCCGCTCCGCCAGTAGCGGTGCCTCCGGCCTCTCCTCCGGCTATTCCGCCACCGGTGCAGGCGCCGGCACCTTCGCATCACAAACGCAAGAAGAAGAAGAAG???CACCACCACCACG???CCGCCCCTGCGCCAACTCCGTCCGCACTGAAAAGCCCGCCTAGTCCTCCACTTGGGAGCCCCGGGCCTTCTACCTCGGCCGATTCCTTCGCTCCCGCCCCTTCACAACCGGTAATCTCCGCCACCATTTATTTTATTAAATCGACTTAATGGCTGTTCAGGATCTGACCGTGGCTGCCTGTTTTTGTTTTTCTTGTTTGCAGAGTGCGGGAATGAAGAGCTCCGCCGCGAGCGTGTGTGGCACGCTGGTCATCCCACA Pinus_ayacahuite_VAR_VEITCII_03S2 ATGGCTCTGCATTGCAAGTTTCAGTAATGGAGAAGAGCCTCTGGTTGATACTGTGTTAGCTACTGCACCGGCGGCGCCCACCACTGCTAAACCACCCACAACTGCACCGGCGGCACCGGTCTCAACTCCGAAACCTCCCACGACCACGCCCGTAGCGCCCGCAGTCGCTCCCACGAAACCGGCTCCGCCCGTAGCGCCAGCCGTTGCTCCCACCAAGCCGGTTCCGCCCGT???????????????????????????????????????GACGGCGCCCACCAAAGCCCCTCCTCCTACCACTAAACCTCCCGCCGTTGCTCCCGCCAAAGCTCCGGTTTCCGCACCGCCGGTGGCTACACCTCCGGTTGCCGTACCCCCAGTGGCTACGCCGCCTGTCGCCGCTCCGCCGGTAGCGGTGCCTCCGGCCTCTCCTCCGGCTATTCCGCCACCGGTGCAAGCGCCGGCACCTTCGCATCACAAACGCAAGAAGAAGAAGAAGAAGCACCACCACCACGGCCCCGCCCCTGCGCCAACTCCGTCCGCACTGAAAAGCCCGCCTAGTCCTCCACTTGGGAGCCCCGGGCCTTCTACCTCGGCCGACTCCTTCGCTCCCGCCCCTTCACAACCGGTAATCTCCG?CACCATTTATTTTATTAAATCGACTTAATGGCTGTTCAGGATCTGACCGTGGCTGCCTGTTTTTGTTTTTCTTGTTTGCAGAGTGCGGGAATGAAGAGCTCCGCCGCGAGCGTGTGTGGCACGCTGGTCATCCAAAC Pinus_chiapensis_01S1 ATGGCTCTGCATTGCAAGTTTCAGTAATGCAGAAGAGCCTCTGGTTGATACTGTGTTAGCTACTGCACCGGCGGCGCCCACCACTGCTAAACCACCCACAACTGCACCGGCGGCACCGGTCTCAACTCCGAAGCCTCCCACGACAACCCCCGTAGCGCCCGCCGTCGCTCCCACGAAACCGACTCCGCCCGTAGCGCCCGCCGTTGCTCCCACCAAGCCGGCTCCGCCCGT???????????????????????????????????????CACGGCTCCCACCAAAGCCCCTCCTCCCACCACTAAACCTCCCGCCGTTGCTCCCGTCAAAGCTCCGGTTTCCGCACCGCCGGTGGCTACGCCTCCCGTTGCCGTACCCCCGGTGGCTACCCCGCCTGTCGCCGCTCCGCCAGTAGCGGTGCCTCCGGCCTCTCCTCCGGCTATTCCGCCACCGGTGCAAGCGCCGGCACCTTCGCATCACAAACGCAAGAAGAAGAAGAAGAAGCACCACCACCACGGCCCCGCCCCTGCGCCAACTCCGTCCGCACTGAAAAGCCCGCCTAGTCCTCCACTTGGGAGCCCCGGGCCTTCTACCTCGGCCGATTCCTTCGCTCCCGCCCCTTCACAACCGGTAATCTCCGCCACCATTTATTTTATTAAATCGACTTGATGGCTGTTCAGGATCTGACCGTGGCTGCCTGTTTTTGTTTTTCTTGTTTGCAGAGTGCGGGAATGAAGAGCTCCGCCGCGAGCGTGTGTGGCACGCTGGTCATCCAAAA Pinus_chiapensis_01S2 ATGGCTCTGCATTGCAAGTTTCAGTAATGCAGAAGAGCCTCTGGTTGATACTGTGTTAGCTACTGCACCGGCGGCGCCCACCACTGCTAAACCACCCACAACTGCACCGGCGGCACCGGTCTCAACTCCGAAGCCTCCCACGACAACCCCCGTAGCGCCCGCCGTCGCTCCCACGAAACCGACTCCGCCCGTAGCGCCCGCCGTTGCTCCCACCAAGCCGGCTCCGCCCGT???????????????????????????????????????CACGGCTCCCACCAAAGCCCCTCCTCCCACCACTAAACCTCCCGCCGTTGCTCCCGTCAAAGCTCCGGTTTCCGCACCGCCGGTGGCTACGCCTCCCGTTGCCGTACCCCCGGTGGCTACCCCGCCTGTCGCCGCTCCGCCAGTAGCGGTGCCTCCGGCCTCTCCTCCGGCTATTCCGCCACCGGTGCAAGCGCCGGCACCTTCGCATCACAAACGCAAGAAGAAGAAGAAGAAGCACCACCACCACGGCCCCGCCCCTGCGCCAACTCCGTCCGCACTGAAAAGCCCGCCTAGTCCTCCACTTGGGAGCCCCGGGCCTTCTACCTCGGCCGATTCCTTCGCTCCCGCCCCTTCACAACCGGTAATCTCCGCCACCATTTATTTTATTAAATCGACTTGATGGCTGTTCAGGATCTGACCGTGGCTGCCTGTTTTTGTTTTTCTTGTTTGCAGAGTGCGGGAATGAAGAGCTCCGCCGCGAGCGTGTGTGGCACGCTGGTCATCCAAAA Pinus_chiapensis_02S1 ATGGCTCTGCATTGCAAGTTTCAGTAATGCAGAAGAGCCTCTGGTTGATACTGTGTTAGCTACTGCACCGGCGGCGCCCACCACTGCTAAACCACCCACAACTGCACCGGCGGCACCGGTCTCAACTCCGAAGCCTCCCACGACAACCCCCGTAGCGCCCGCCGTCGCTCCCACGAAACCGACTCCGCCCGTAGCGCCCGCCGTTGCTCCCACCAAGCCGGCTCCGCCCGT???????????????????????????????????????CACGGCTCCCACCAAAGCCCCTCCTCCCACCACTAAACCTCCCGCCGTTGCTCCCGTCAAAGCTCCGGTTTCCGCACCGCCGGTGGCTACGCCTCCCGTTGCCGTACCCCCGGTGGCTACCCCGCCTGTCGCCGCTCCGCCAGTAGCGGTGCCTCCGGCCTCTCCTCCGGCTATTCCGCCACCGGTGCAAGCGCCGGCACCTTCGCATCACAAACGCAAGAAGAAGAAGAAGAAGCACCACCA???CGGCTCCGCCCCTGCGCCGACTCCGTCCGCATTGAAAAGCCCGCCCAGTCCTCCACTTGGGAGCCCCGGGCCTTCTACCTCGGCCGATTCCTTCGCTCCCGCCCCTTCACAACCGGTAATCTCCACCACCATTTATTTTATTAAATCGACTTAATGGCTGTTCAGGATCTGACCGTGGCTGCCTGTTTTTGTTTTTCCTTTTTGCAGAGTGCGGGAATGAAGAGCTCCGCCGCGAGCGTGTGTGGCACGCTGGTCATCCACAA Pinus_chiapensis_05N ATGGCTCTGCATTGCAAGTTTCAGTAATGCAGAAGAGCCTCTGGTTGATACTGTGTTAGCTACTGCACCGGCGGCGCCCACCACTGCTAAACCACCCACAACTGCACCGGCGGCACCGGTCTCAACTCCGAAGCCTCCCACGACAACCCCCGTAGCGCCCGCCGTCGCTCCCACGAAACCGACTCCGCCCGTAGCGCCCGCCGTTGCTCCCACCAAGCCGGCTCCGCCCGT???????????????????????????????????????CACGGCTCCCACCAAAGCCCCTCCTCCCACCACTAAACCTCCCGCCGTTGCTCCCGTCAAAGCTCCGGTTTCCGCACCGCCGGTGGCTACGCCTCCCGTTGCCGTACCCCCGGTGGCTACCCCGCCTGTCGCCGCTCCGCCAGTAGCGGTGCCTCCGGCCTCTCCTCCGGCTATTCCGCCACCGGTGCAAGCGCCGGCACCTTCGCATCACAAACGCAAGAAGAAGAAGAAGAAGCACCACCA???CGGCTCCGCCCCTGCGCCGACTCCGTCCGCATTGAAAAGCCCGCCCAGTCCTCCACTTGGGAGCCCCGGGCCTTCTACCTCGGCCGATTCCTTCGCTCCCGCCCCTTCACAACCGGTAATCTCCACCACCATTTATTTTATTAAATCGACTTAATGGCTGTTCAGGATCTGACCGTGGCTGCCTGTTTTTGTTTTTCCTTTTTGCAGAGTGCGGGAATGAAGAGCTCCGCCGCGAGCGTGTGTGGCACGCTGGTCATCCACAA Pinus_chiapensis_35S1 ATGGCTCTGCATTGCAAGTTTCAGTAATGCAGAAGAGCCTCTGGTTGATACTGTGTTAGCTACTGCACCGGCGGCGCCCACCACTGCTAAACCACCCACAACTGCACCGGCGGCACCGGTCTCAACTCCGAAGCCTCCCACGACAACCCCCGTAGCGCCCGCCGTCGCTCCCACGAAACCGACTCCGCCCGTAGCGCCCGCCGTTGCTCCCACCAAGCCGGCTCCGCCCGT???????????????????????????????????????CACGGCTCCCACCAAAGCCCCTCCTCCCACCACTAAACCTCCCGCCGTTGCTCCCGTCAAAGCTCCGGTTTCCGCACCGCCGGTGGCTACGCCTCCCGTTGCCGTACCCCCGGTGGCTACCCCGCCTGTCGCCGCTCCGCCAGTAGCGGTGCCTCCGGCCTCTCCTCCGGCTATTCCGCCACCGGTGCAAGCGCCGGCACCTTCGCATCACAAACGCAAGAAGAAGAAGAAGAAGCACCACCA???CGGCTCCGCCCCTGCGCCGACTCCGTCCGCATTGAAAAGCCCGCCCAGTCCTCCACTTGGGAGCCCCGGGCCTTCTACCTCGGCCGATTCCTTCGCTCCCGCCCCTTCACAACCGGTAATCTCCACCACCATTTATTTTATTAAATCGACTTAATGGCTGTTCAGGATCTGACCGTGGCTGCCTGTTTTTGTTTTTCCTTTTTGCAGAGTGCGGGAATGAAGAGCTCCGCCGCGAGCGTGTGTGGCACGCTGGTCATCCACAA Pinus_chiapensis_38S1 ATGGCTCTGCATTGCAAGTTTCAGTAATGCAGAAGAGCCTCTGGTTGATACTGTGTTAGCTACTGCACCGGCGGCGCCCACCACTGCTAAACCACCCACAACTGCACCGGCGGCACCGGTCTCAACTCCGAAGCCTCCCACGACAACCCCCGTAGCGCCCGCCGTCGCTCCCACGAAACCGACTCCGCCCGTAGCGCCCGCCGTTGCTCCCACCAAGCCGGCTCCGCCCGT???????????????????????????????????????CACGGCTCCCACCAAAGCCCCTCCTCCCACCACTAAACCTCCCGCCGTTGCTCCCGTCAAAGCTCCGGTTTCCGCACCGCCGGTGGCTACGCCTCCCGTTGCCGTACCCCCGGTGGCTACCCCGCCTGTCGCCGCTCCGCCAGTAGCGGTGCCTCCGGCCTCTCCTCCGGCTATTCCGCCACCGGTGCAAGCGCCGGCACCTTCGCATCACAAACGCAAGAAGAAGAAGAAGAAGCACCACCACCACGGCCCCGCCCCTGCGCCAACTCCGTCCGCACTGAAAAGCCCGCCTAGTCCTCCACTTGGGAGCCCCGGGCCTTCTACCTCGGCCGATTCCTTCGCTCCCGCCCCTTCACAACCGGTAATCTCCGCCACCATTTATTTTATTAAATCGACTTGATGGCTGTTCAGGATCTGACCGTGGCTGCCTGTTTTTGTTTTTCTTGTTTGCAGAGTGCGGGAATGAAGAGCTCCGCCGCGAGCGTGTGTGGCACGCTGGTCATCCAAAA Pinus_chiapensis_39S1 ATGGCTCTGCATTGCAAGTTTCAGTAATGCAGAAGAGCCTCTGGTTGATACTGTGTTAGCTACTGCACCGGCGGCGCCCACCACTGCTAAACCACCCACAACTGCACCGGCGGCACCGGTCTCAACTCCGAAGCCTCCCACGACAACCCCCGTAGCGCCCGCCGTCGCTCCCACGAAACCGACTCCGCCCGTAGCGCCCGCCGTTGCTCCCACCAAGCCGGCTCCGCCCGT???????????????????????????????????????CACGGCTCCCACCAAAGCCCCTCCTCCCACCACTAAACCTCCCGCCGTTGCTCCCGTCAAAGCTCCGGTTTCCGCACCCCCGGTGGCTACGCCTCCCGTTGCCGTACCCCCGGTGGCTACCCCGCCTGTCTCCGCTCCGCCAGTAGCGGTGCCTCCGGCCTCTCCTCCGGCTATTCCGCCACCGGTGCAAGCGCCGGCACCTTCGCATCACAAACGCAAGAAGAAGAAGAAGAAGCACCACCACCACGGCCCCGCCCCTGCGCCAACTCCGTCCGCACTGAAAAGCCCGCCTAGTCCTCCACTTGGGAGCCCCGGGCCTTCTACCTCGGCCGATTCCTTCGCTCCCGCCCCTTCACAACCGGTAATCTCCGCCACCATTTATTTTATTAAATCGACTTGATGGCTGTTCAGGATCTGACCGTGGCTGCCTGTTTTTGTTTTTCTTGTTTGCAGAGTGCGGGAATGAAGAGCTCCGCCGCGAGCGTGTGTGGCACGCTCGTCATCCAAAA Pinus_chiapensis_41S1 ATGGCTCTGCATTGCAAGTTTCAGTAATGCAGAAGAGCCTCTGGTTGATACTGTGTTAGCTACTGCACCGGCGGCGCCCACCACTGCTAAACCACCCACAACTGCACCGGCGGCACCGGTCTCAACTCCGAAGCCTCCCACGACAACCCCCGTAGCGCCCGCCGTCGCTCCCACGAAACCGACTCCGCCCGTAGCGCCCGCCGTTGCTCCCACCAAGCCGGCTCCGCCCGT???????????????????????????????????????CACGGCTCCCACCAAAGCCCCTCCTCCCACCACTAAACCTCCCGCCGTTGCTCCCGTCAAAGCTCCGGTTTCCGCACCGCCGGTGGCTACGCCTCCCGTTGCCGTACCCCCGGTGGCTACCCCGCCTGTCGCCGCTCCGCCAGTAGCGGTGCCTCCGGCCTCTCCTCCGGCTATTCCGCCACCGGTGCAAGCGCCGGCACCTTCGCATCACAAACGCAAGAAGAAGAAGAAGAAGCACCACCACCACGGCCCCGCCCCTGCGCCAACTCCGTCCGCACTGAAAAGCCCGCCTAGTCCTCCACTTGGGAGCCCCGGGCCTTCTACCTCGGCCGATTCCTTCGCTCCCGCCCCTTCACAACCGGTAATCTCCGCCACCATTTATTTTATTAAATCGACTTGATGGCTGTTCAGGATCTGACCGTGGCTGCCTGTTTTTGTTTTTCTTGTTTGCAGAGTGCGGGAATGAAGAGCTCCGCCGCGAGCGTGTGTGGCACGCTGGTCATCCAAAA Pinus_gerardiana ATGGCTCTGCATTGCAAATTTCAGTAATGGAGAAGAGCCTCTGGTTGATACTGTGTTAGCTACTGCACCGGCGGCGCCCACCACTGCTAAACCACCCACAACTGCACCGGCGGCACCGGTCTCAACTCCGAAGCCTCCCACGACAACGCCCGTAGCGCCCGCCGTCGCTCCCACGAAACCGACTCCGCCCGTAGCGCCCGCCGTCGCTCCCACGAAACCGGCTCCGCCCGTAGCGCCCGCCGTCGCTCCCACCAAGCCGGCTCCGCCCGTCACGGCGCCCACCAAAGCCCCTCCTCCCACCACTAAACCTCCCGCCGTTGCTCCCGTCAAAGCTCCGGTTTCCGCACCGCCGGTGGCTACGCCTCCGGTTGCCGTACCCCCAGTGGCTACTCCGCCTGTCGCTGCTCCGCCAGTAGCGGTGCCTCCGGCCTCTCCTCCGGCTATTCCGCCACCGGTGCAGGCGCCGGCACCTTCGCACCACAAACACAAGAAGAAGAAGAAGAAGCACCACCACCACGGCCCCACCCCTGCGCCAACTCCATCCGCACTGAAAAGCCCGCCTAGTCCTCCACTTGGGAGCCCCGGGCCTTCTACCTCGGCCGATTCCTTCGCTCCCGCCCCGTCACAGCCGGTAATCTCCGCCACCATTTATTTTATTACATCGACTTAATGGCTGTTCAGGATCTGACCGTAGCTGCCTGTTTTTGTTTTTCCTTTTTGCAGAGTGCGGGAATGAAGAGCTCCGCCGCGAGCGTGTGTGGCACGCTGGTCATCAAAAA Pinus_monticola_01S1_02S3 ATGGCTCTGCATTGCAAGTTTCATTAATGGAGAAGAGCCTCTGGTTGATACTGTGTTAGCTACTGCACCGGCGGCGCCCACCACTGCTAAACCACCCACAACTGCACCGGCGGCACCGGTCTCAACTCCGAAGCCTCCCACGACAACCCCCGTAGCGCCCGCCGTCGCTCCCACGAAACCGACTCCGCCCGTAGCGCCCGCCGTTGCTCCCACCAAGCCGGCTCCGCCCGT???????????????????????????????????????CACGGCTCCCACCAAAGCCCCTCCTCCCACCACTAAACCTCCCGCCGTAGCTCCCGTCAAAGCTCCGGTTTCCGCACCGCCGGTGGCTACGCCTCCGGTTGCCGTACCCCCAGTGGCTACGCCGCCTGTCGCCGCTCCGCCAGTAGCGGTGCCTCCGGCCTCTCCTCCGGCTATTCCGCCACCGGTGCAAGCGCCGGCACCTTCGCATCACAAACGCAAGAAGAAGAAGAAGAAGCACCACCACCACGGCCCCGCCCCTGCGCCAACTCCGTCCGCACTGAAAAGCCCGCCTAGTCCTCCACTTGGGAGCCCCGGGCCTTCTACCTCGGCCGATTCCTTCGCTCCCGCCCCTTCACAACCGGTAATCTCCG?CACCATTTATTTTATTAAATCGACTTAATGGCTGTTCAGGATCTGACCGTGGCTGCCTGTTTTTGTTTTTCTTGTTTGCAGAGTGCGGGAATGAAGAGCTCCGCCGCGAGCGTGTGTGGCACGCTGGTCATCCAAAC Pinus_monticola_02S1_07S1_05S1 ATGGCTCTGCATTGCAAGTTTCATTAATGGAGAAGAGCCTCTGGTTGATACTGTGTTAGCTACTGCACCGGCGGCGCCCACCACTGCTAAACCACCCACAACTGCACCGGCGGCACCGGTCTCAACTCCGAAGCCTCCCACGACAACCCCCGTAGCGCCCGCCGTCGCTCCCACGAAACCGACTCCGCCCGTAGCGCCCGCCGTTGCTCCCACCAAGCCGGCTCCGCCCGT???????????????????????????????????????CACGGCTCCCACCAAAGCCCCTCCTCCCACCACTAAACCTCCCGCCGTTGCTCCCGTCAAAGCTCCGGTTTCCGCACCGCCGGTGGCTACGCCTCCGGTTGCCGTACCCCCAGTGGCTACGCCGCCTGTCGCCGCTCCGCCAGTAGCGGTGCCTCCGGCCTCTCCTCCGGCTATTCCGCCACCGGTGCAAGCGCCGGCACCTTCGCATCACAAACGCAAGAAGAAGAAGAAGAAGCACCACCACCACGGCCCCGCCCCTGCGCCAACTCCGTCCGCACTGAAAAGCCCGCCTAGTCCTCCACTTGGGAGCCCCGGGCCTTCTACCTCGGCCGATTCCTTCGCTCCCGCCCCTTCACAACCGGTAATCTCCG?CACCATTTATTTTATTAAATCGACTTAATGGCTGTTCAGGATCTGACCGTGGCTGCCTGTTTTTGTTTTTCTTGTTTGCAGAGTGCGGGAATGAAGAGCTCCGCCGCGAGCGTGTGTGGCACGCTGGTCATCCAAAC Pinus_monticola_04S1 ATCGCTCTGCATTGCAAGTTTCAGTAATGGAGAAGAGCCTCTGGTTGATACTGTGTTAGCTACTGCACCGGCGGCGCCCACCACTGCTAAACCACCCACAACTGCACCGGCGGCACCGGTCTCAACTCCGAAGCCTCCCACGACAACGCCCGTAGCGCCCGCCGTCGCTCCCACGAAACCAACTCCGCCCGTAGCGCCCGCCGTTGCTCCCACCAAGCCGGCTCCGCCCGT???????????????????????????????????????CACGGCGCCCACCAAAGCTCCTCCTCCCACCACTAAACCTCCCGCCGTTGCTCCCGCCAAAGCTCCGGTTTCCGCACCGCCGGTGGCTACACCTCCGGTTGCCGTACCCCCAGTGGCTACGCCGCCTGTCGCCGCTCCGCCGGTAGCGGTGCCTCCGGCCTCTCCTCCGGCTATTCCGCCACCGGTGCAAGCGCCGGCACCTTCGCATCACAAACGCAAGAAGAAGAAGAAGAAGCACCACCACCACGGCCCCGCCCCTGCGCCAACTCCGTCCGCACTGAAAAGCCCGCCTAGTCCTCCACTTGGGAGCCCCGGGCCTTCTACCTCGGCCGATTCCTTCGCTCCCGCCCCTTCACAACCGGTAATCTCCGCCACCATTTATTTTATTAAATCGACTTAATGGCTGTTCAGGATCTGACCGTGGCTGCCTGTTTTTGTTTTTCTTTTTCGCAGAGTGCGGGAATGAAGAGCTCCGCCGCGACCGTGTGTGGCACGCTGGTCATCCAAAA Pinus_monticola_06S1 ATGGCTCTGCATTGCAAGTTTCATTAATGGAGAAGAGCCTCTGGTTGATACTGTGTTAGCTACTGCACCGGCGGTGCCCACCACTGCTAAACCACCCACAACTGCACCGGCGGCACCGGTCTCAACTCCGAAGCCTCCCACGACAACCCCCGTAGCGCCCGCCGTCGCTCCCACGAAACCGACTCCGCCCGTAGCGCCCGCCGTTGCTCCCACCAAGCCGGCTCCGCCCGT???????????????????????????????????????CACGGCTCCCACCAAAGCCCCTCCTCCCACCACTAAACCTCCCGCCGTTGCTCCCGTCAAAGCTCCGGTTTCCGCACCGCCGGTGGCTACGCCTCCGGTTGCCGTACCCCCAGTGGCTACGCCGCCTGTCGCCGCTCCGCCAGTAGCGGTGCCTCCGGCCTCTCCTCCGGCTATTCCGCCACCGGTGCAAGCGCCGGCACCTTCGCATCACAAACGCAAGAAGAAGAAGAAGAAGCACCACCACCACGGCCCCGCCCCTGCGCCAACTCCGTCCGCACTGAAAAGCCCGCCTAGTCCTCCACTTGGGAGCCCCGGGCCTTCTACCTCGGCCGATTCCTTCGCTCCCGCCCCTTCACAACCGGTAATCTCCG?CACCATTTATTTTATTAAATCGACTTAATGGCTGTTCAGGATCTGACCGTGGCTGCCTGTTTTTGTTTTTCTTGTTTGCAGAGTGCGGGAATGAAGAGCTCCGCCGCGAGCGTGTGTGGCACGCTGGTCATCCAAAC Pinus_monticola_13S1 ATGGCTCTGCATTGCAAGTTTCAGTAATGCAGAAGAGCCTCTGGTTGATACTGTGTTAGCTACTGCACCGGCGGCGCCCACCACTGCTAAACCACCCACAACTGCACCGGCGGCACCGGTCTCAACTCCGAAGCCTCCCACGACAACCCCCGTAGCGCCCGCCGTCGCTCCCACGAAACCGACTCCGCCCGTAGCGCCCGCCGTTGCTCCCACCAAGCCGGCTCCGCCCGT???????????????????????????????????????CACGGCTCCCACCAAAGCTCCTCCTCCCACCACTAAACCTCCCGCTGTTGCTCCCGCCAAAGCTCCGGTTTCCGCACCGCCGGTGGCTACGCCTCCCGTTGCCGTACCCCCGGTGGCTACTCCGCCTGTCGCCGCTCCGCCAGTAGCGGTGCCTCCGGCCTCTCCTCCGGCTATTCCGCCACCGGTGCAGGCGCCGGCACCTTCGCATCACAAACACAAGAAGAAGAAGAAGAAGCACCACCA???CGGCTCCGCCCCTGCGCCGACTCCGTCCGCACTGAAAAGCCCGCCCAGTCCTCCACTTGGGAGCCCCGGGCCTTCTACCTCGGCCGATTCCTTCGCTCCCGCCCCTTCACAACCGGTAATCTCCGCCACCATTTATTTTATTAAATCGACTTAATGGCTGTTCAGGATCTGACCGTGGCTGCCTGTTTTTGTTTTTGTTTTTCGCAGAGTGCGGGAATGAAGAGCTCCGCCGCAAGCGTGTGTGGCACGCTGGTCATCCACAA Pinus_monticola_16S1 ATGGCTCTGCATTGCAAGTTTCAGTAATGCAGAAGAGCCTCTGGTTGATACTGTGTTAGCTACTGCACCGGCGGCGCCCACCACTGCTAAACCACCCACAACTGCACCGGCGGCACCGGTCTCAACTCCGAAGCCTCCCACGACAACGCCCGTAGCGCCCGCCGTCGCTCCCACGAAACCGGCTCCGCCCGTAGCGCCAGCCGTTGCTCCCACCAAGCCGGCTCCGCCCGT???????????????????????????????????????GACGGCGCCCACGAAAGCCCCTCCTCCCACCACTAAACCTCCCGCCGTTGCTCCCGCCAAAGCTCCGGTTTCCGCACCGCCGGTGGCTACGCCTCCGGTTGCCGTACCCCCGGTGGCTACTCCGCCTGTCGCCGCTCCGCCAGTAGCGGTGCCTCCGGCCTCTCCTCCGGCTATTCCGCCACCGGTGCAGGCGCCGGCACCTTCGCATCACAAACGCAAGAAGAAGAAGAAGAAGCACCACCACCACGGCCCCGCCCCTGCGCCAACTCCGTCCGCACTGAAAAGCCCGCCTAGTCCTCCACTTGGGAGCCCCGGGCCTTCTACCTCGGCCGATTCCTTCGCTCCCGCCCCTTCACAACCGGTAATCTCCGCCACCATTTATTTTATTAAATCGACTTCATGGCTGTTCAGGATCTGACCGTGGCTGCCTGTTTTTCTTTTTCTTTTTCGCAGAGTGCGGGAATGAAGAGCTCCGCCGCGAGCGTGTGTGGCACGCTGGTCATCCAAAA Pinus_squamata ATGGCTCTGCATTGCAAGTTTCAGTAATGGAGAAGAGCCTCTGCTTGATACTGTGTTAGCTACTGCACCGGCGGCGCCCACCACTGCTAAACCACCCACAACTGCACCGGCGGCACCGGTCTCAACTCCGAAGCCTCCCACGACAACGCCCGTAGCGCCCGCCGTCGCTCCCACGAAACCGACTCCGCCCGTAGCTCCCGCCGTCGCTCCCACGAAACCGGCTCCGCCCGTAGCGCCCGCCGTGGCTCCCACCAAGCCAGCTCCGCCGGTCACGGCGCCCACCAAAGCCCCTCCTCCCACCACTAAACCTCCCGCCGTTGCTCCCGTCAAAGCTCCGGTTTCCGCACCGCCGGTGGCTACGCCTCCGGTTGCCGTACCCCCAGTGGCTACTCCGCCTGTCGCTGCTCCGCCAGTAGCGGTGCCTCCGGCCTCTCCTCCGGCTATTCCGCCACCGGTGCAGGCGCCGGCACCTTCGCACCACAAACACAAGAAGAAGAAGAAGAAGCACCACCACCACGGCCCCGCCCCTGCGCCAACTCCATCCGCACTGAAAAGTCCGCCTAGTCCTCCACTCGGGAGCCCCGGGCCTTCTACCTCGGCCGATTCGTTCGCTCCCGCCCCTTCACAACCGGTAATCTCCGCCACCATTTAGTTTATTAAATCGATTTAATGGCTGTTCAGGATCTGACCGTAGCTGCCTGTTTTTCTTTTTCTTTTTTGCAGAGTGCGGGAATGAAGAGCTCCGCCGCGAGCGTGTGTGGCACGGTGGTCATCAAAAA Pinus_strobus_01S1 ATGGCTCTGCATTGCAAGTTTCAGTAATGGAGAAAAGCCTCTGGTTGATACTGTGTTAGCTACTGCACCGGCGGCGCCCACCACTGCTAAACCACCCACAACTGCACCGGCGGCACCGGTCTCAACTCCGAAGCCTCCCACGACAACGCCCGTAGCGCCCGCCGTCGCTCCCACGAAACCGACTCCGCCCGTAGCGCCCGCCGTTGCTCCCACCAAGCCGGCTCCACCCGT???????????????????????????????????????CACGGCGCCCACCAAAGCTCCTCCTCCCACCACTAAACCACCCGCCGTTGCTCCCGCCAAAGCTCCGGTTTCCGCACCGCCGGTGGCTACGCCTCCGGTTGCCGTACCCCCGGTGGCTACTCCGCCTGTCGCCGCTCCGCCAGTAGCGGTGCCTCCGGCCTCTCCTCCGGCTATTCCGCCACCGGTGCAGGCGCCGGCACCTTCGCATCACAAACGCAAGAAGAAGAAGAAG???CACCACCACCACG???CCGCCCCTGCGCCAACTCCGTCCGCACTGAAAAGCCCGCCTAGTCCTCCACTTGGGAGCCCCGGGCCTTCTACCTCGGCCGATTCCTTCGCTCCCACCCCTTCACAACCGGTAATCTCCGCCACCATTTATTTTATTAAATCGACTTAATGGCTGTTCAGGATCTGACCGTGGCTGCCTGTTTTTGTTTTTCTTGTTTGCAGAGTGCGGGAATGAAGAGCTCCGCCGCGAGCGTGTGTGGCACGCTGGTCATCCCACA Pinus_strobus_02S1_10S1 ATGGCTCTGCATTGCAAGTTTCAGTAATGGAGAAAAGCCTCTGGTTGATACTGTGTTAGCTACTGCACCGGCGGCGCCCACCACTGCTAAACCACCCACAACTGCACCGGCGGCACCGGTCTCAACTCCGAAGCCTCCCACGACAACGCCCGTAGCGCCCGCCGTCGCTCCCACGAAACCGACTCCGCCCGTCGCGCCCGCCGTTGCTCCCACCAAGCCGGCTCCACCCGT???????????????????????????????????????CACGGCGCCCACCAAAGCTCCTCCTCCCACCACTAAACCTCCCGCCGTTGCTCCCGCCAAAGCTCCGGTTTCCGCACCGCCGGTGGCTACGCCTCCGGTTGCCGTACCCCCGGTGGCTACTCCGCCTGTCGCCGCTCCGCCAGTAGCGGTGCCTCCGGCCTCTCCTCCGGCTATTCCGCCACCGGTGCAGGCGCCGGCACCTTCGCATCACAAACGCAAGAAGAAGAAGAAG???CACCACCACCACG???CCGCCCCTGCGCCAACTCCGTCCGCACTGAAAAGCCCGCCTAGTCCTCCACTTGGGAGCCCCGGGCCTTCTACCTCGGCCGATTCCTTCGCTCCCGCCCCTTCACAACCGGTAATCTCCGCCACCATTTATTTTATTAAATCGACTTAATGGCTGTTCAGGATCTGACCGTGGCTGCCTGTTTTTGTTTTTCTTGTTTGCAGAGTGCGGGAATGAAGAGCTCCGCCGCGAGCGTGTGTGGCACGCTGGTCATCCCACA Pinus_strobus_03S1_22S3_26Nh_09S1_05S1 ATGGCTCTGCATTGCAAGTTTCAGTAATGGAGAAAAGCCTCTGGTTGATACTGTGTTAGCTACTGCACCGGCGGCGCCCACCACTGCTAAACCACCCACAACTGCACCGGCGGCACCGGTCTCAACTCCGAAGCCTCCCACGACAACGCCCGTAGCGCCCGCCGTCGCTCCCACGAAACCGACTCCGCCCGTAGCGCCCGCCGTTGCTCCCACCAAGCCGGCTCCACCCGT???????????????????????????????????????CACGGCGCCCACCAAAGCTCCTCCTCCCACCACTAAACCTCCCGCCGTTGCTCCCGCCAAAGCTCCGGTTTCCGCACCGCCGGTGGCTACGCCTCCGGTTGCCGTACCCCCGGTGGCTACTCCGCCTGTCGCCGCTCCGCCAGTAGCGGTGCCTCCGGCCTCTCCTCCGGCTATTCCGCCACCGGTGCAGGCGCCGGCACCTTCGCATCACAAACGCAAGAAGAAGAAGAAG???CACCACCACCACG???CCGCCCCTGCGCCAACTCCGTCCGCACTGAAAAGCCCGCCTAGTCCTCCACTTGGGAGCCCCGGGCCTTCTACCTCGGCCGATTCCTTCGCTCCCGCCCCTTCACAACCGGTAATCTCCGCCACCATTTATTTTATTAAATCGACTTAATGGCTGTTCAGGATCTGACCGTGGCTGCCTGTTTTTGTTTTTCTTGTTTGCAGAGTGCGGGAATGAAGAGCTCCGCCGCGAGCGTGTGTGGCACGCTGGTCATCCCACA Pinus_strobus_04S1 ATGGCTCTGCATTGCAAGTTTCAGTAATGGAGAAAAGCCTCTGGTTGATACTGTGTTAGCTACTGCACCGGCGGCGCCCACCACTGCTAAACCACCCACAACTGCACCGGCGGCACCGGTCTCAACTCCGAAGCCTCCCACGACAACGCCCGTAGCGCCCGCCGTCGCTCCCACGAAACCGACTCCGCCCGTAGCGCCCGCCGTTGCTCCCACCAAGCCGGCTCCACCCGT???????????????????????????????????????CACGGCGCCCACCAAAGCTCCTCCTCCCACCACTAAACCTCCCGCCGTTGCTCCCGCCAAAGCTCCGGTTTCCGCACCGCCGGTGGCTACGCCTCCGGTTGCCGTACCCCCGGTGGCTACTCCGCCTGTCGCCGCTCCGCCAGTAGCGGTGCCTCCGGCCTCTCCTCCGGCTATTCCGCCACCGGTGCAGGCGCCGGCACCTTCGCATCACAAACGCAAGAAGAAGAAGAAG???CACCACCACCACG???CCGCCCCTGCGCCAACTCCGTCCTCACTGAAAAGCCCGCCTAGTCCTCCACTTGGGAGCCCCGGGCCTTCTACCTCGGCCGATTCCTTCGCTCCCGCCCCTTCACAACCGGTAATCTCCGCCACCATTTATTTTATTAAATCGACTTAATGGCTGTTCAGGATCTGACCGTGGCTGCCTGTTTTTGTTTTTCTTGTTTGCAGAGTGCGGGAATGAAGAGCTCCGCCGCGAGCGTGTGTGGCACGCTGGTCATCCCACA Pinus_strobus_11S2 ATGGCTCTGCATTGCAAGTTTCAGTAATGGAGAAAAGCCTCTGGTTGATACTGTGTTAGCTACTGCACCGGCGGCGCCCACCACTGCTAAACCACCCACAACTGCACCGGCGGCACCGGTCTCAACTCCGAAGCCTCCCACGACAACGCCCGTAGCGCCCGCCGTCGCTCCCACGAAACCGACTCCGCCCGTCGCGCCCGCCGTTGCTCCCACCAAGCCGGCTCCACCCGT???????????????????????????????????????CACGGCGCCCACCAAAGCTCCTCCTCCCACCACTAAACCTCCCGCCGTTGCTCCCGCCAAAGCTCCGGTTTCCGCACCGCCGGTGGCTACGCCTCCGGTTGCCGTACCCCCGGTGGCTACTCCGCCTTTCGCCGCTCCGCCAGTAGCGGTGCCTCCGGCCTCTCCTCCGGCTATTCCGCCACCGGTGCAGGCGCCGGCACCTTCGCATCACAAACGCAAGAAGAAGAAGAAG???CACCACCACCACG???CCGCCCCTGCGCCAACTCCGTCCGCACTGAAAAGCCCGCCTAGTCCTCCACTTGGGAGCCCCGGGCCTTCTACCTCGGCCGATTCCTTCGCTCCCGCCCCTTCACAACCGGTAATCTCCGCCACCATTTATTTTATTAAATCGACTTAATGGCTGTTCAGGATCTGACCGTGGCTGCCTGTTTTTGTTTTTCTTGTTTGCAGAGTGCGGGAATGAAGAGCTCCGCCGCGAGCGTGTGTGGCACGCTGGTCATCCCACA ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = AGP6) = N: 1-779; CODONPOSSET CodonPositions (CHARACTERS = AGP6) = N: 1-779; END; [ The following blocks are output data for analysis step 3198 ] BEGIN TREES; TITLE Tb7971; LINK TAXA = TaxaForAnalysisStep3198; TREE Fig._4.1 = [&R] ((((Pinus_ayacahuite_VAR_VEITCII_01S1,Pinus_ayacahuite_04S2_03S3,Pinus_ayacahuite_09S2_12S1_15S2,Pinus_strobus_01S1,(Pinus_strobus_02S1_10S1,Pinus_strobus_11S2),Pinus_strobus_03S1_22S3_26Nh_09S1_05S1,Pinus_strobus_04S1),Pinus_monticola_16S1),(((Pinus_ayacahuite_VAR_VEITCII_03S2,Pinus_ayacahuite_18S2),Pinus_monticola_04S1),(((Pinus_chiapensis_01S1,Pinus_chiapensis_01S2,Pinus_chiapensis_38S1,Pinus_chiapensis_39S1,Pinus_chiapensis_41S1),((Pinus_chiapensis_02S1,Pinus_chiapensis_05N,Pinus_chiapensis_35S1),Pinus_monticola_13S1)),(Pinus_monticola_01S1_02S3,Pinus_monticola_02S1_07S1_05S1,Pinus_monticola_06S1)))),(Pinus_gerardiana,Pinus_squamata)); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr767] END;