#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 12, 2025; 11:18 GMT TreeBASE (cc) 1994-2008 Study reference: Yoder A.D., & Yang Z. 2004. Divergence dates for Malagasy lemurs estimated from multiple gene loci: geological and evolutionary context. Molecular Ecology, 13: 757-773. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S1153] [ The following blocks are input data for analysis step 2087 ] BEGIN TAXA; TITLE TaxaForAnalysisStep2087; DIMENSIONS NTAX=21; TAXLABELS Callithrix_jacchus Canis_lupus Cercopithecus Cheirogaleus Colobus_guereza Daubentonia_madagascariensis Erythrocebus Eulemur_fulvus_albifrons Eulemur_fulvus_collaris Eulemur_fulvus_rufus Eulemur_macaco_flavifrons Eulemur_macaco_macaco Felis_silvestris Hapalemur_griseus Homo_sapiens Lemur_catta Macaca_fuscata Saguinus_sp. Scalopus_aquaticus Varecia_variegata_rubra Varecia_variegata_variegata ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2448] TITLE 'Transthyretin (intron 1)'; LINK TAXA = TaxaForAnalysisStep2087; DIMENSIONS NCHAR=901; 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 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Callithrix_jacchus CCTGAAGTAGAAGTGG-TCCTTCTGGCTTTGCCAACCAACTTTTGTTACTAGGGCAAGGGTATTCAGCATCTG-TTTTAAATATCATTGATTAGAACTTCAAAAAGAATGAAGCTCCGCTGAGCTTGCTGAGCTTACTGAGCTGGGACTTGAATTCTGGACATTCTGCCTCATAGC-TTTGGTGCATTGGGTTTGCAAAG-----TCTGGTACCTCAATTTCCTCAGATAGATGATAGAAATAAAGATGTGATATTAAGGAAGATGTTAATACTGAATTTTCAGAAAAGCATCCCTTTATCAAATGTATTTGGGGGG-CAAACCGCATGAGATTATATTCTGGCCCTATAGCTAGTCAAAATGTATTTATTGATTAATCTTTAAAAAGGCT-GGTGA-GTAATATTCTAGATATCTATCTAATTCTTAAATCCTCTAGAAGAATTAATTAATACTATAAAATGGGTCAGGATGTAGA-----CTGACATTATTTTATAACAACCGGTAAGAGGGAGCGACTATGG-CAACAACT----AAAATGATCTCAGG--GAAAACTC---TTTGGCCCTATGT-ATGGTACATTACATCTTTTCAGTGATTGCACTCAAATGGAGAGGCTTAACAAAGCAACTATCCTCAGGGGGCCAATTTTCTCCCTTAAAATTCATTATACACATCCCT-GGTTGATAGCAGCATGTCTGGAGGCAGAAACCATTCTTGCCTTGGAAATAATTATGTCTGTGTTATA--CTGCATAGGGAAGCTCAGTAATTGTCAACACTTATGTT-CCTGATAATGGGATCAGTGTGTAATTCTTGCTTTGTTCCAGATTTCTAATACCATAAACCATAAATCCTTTCACTCT-GATCAATGTTGTTAACTTCTCATTTGT Canis_lupus GTTGAAGTGGAAGTGACTTCTTTTGGCTCTGCCAGCTGGCTTTTGTTGCTAGGACAAGGGTACCCAGCATCAACTCTTAAATCTCATTGATGCAAACCTCAGACTGAATCAAGTTCTGC---------AGAGCTCACTGAACTGAGGCTTGGACCCTGGGTGCTCCCTGCTCTTGC-TTTGGTGCCCTGGCTTTACAGTGCCTGGCTCCTCCACTCCATTCCCTCAGAGAGATGGTAGAACTAAAGGTGTGATATTCATGAAGCCACCGATATTATGTTTTCAGAAATGCATCCTTTCATAAAGCTTGTTT--------------------------------CTTTTCAGCTAATCTAAAGGTATTGATTGATTGATTTTTGCAA-GGCTTGGCAG-ACACTGTTCTAATCAAATACCTAATTCTTAAGTCCTCTAAAAGAATTAACTCATACTATAAAATGGCCCATGAAACAGCC-----TGACATTATTTTGCAGCCAGTGGA-GGGAATTACTACAGCAACAGCCGACT----ACAATGCTCTCGGGGAAAAACTAACTATTTGGTCCTAT-----GGCACATTATACCTTTTCAGTAATTCCACTCAAATAGTGAGGCTTAACAAAGCAACTCTTCTCAAAGGGCCTACTTTCTCCCTTAAAATTCATTATACACGTCCCT-GGTCAATTGTAGCGTGTCTGGAGACAGAAATCAGCTTTGCTGTGGAAGCAATCATGTCTG-GTCACA--CTGAGAAGGGGAGCTCATTAACTATCAACACTTGCATT-GCTGGAAATGGAATTGGCATGTACTTTTTACCTTGTTCCAGATTTCTAGCACCATAAAGAACAGATCCTTTTAGGGGCACCTGGATAGCTCAGTTGGTTAAGCAT Cercopithecus AATGAAGTAGGAGTGACTCCTTCCAGCTTTACCAACCAGCTTTTGTTACTAGGGCAAGGGTGCCCAGCATCTA-TTTTTAATATCATTAATTCAAACTTCAA-AAGAATGAAGTTCCAC---------TGAGCTTACTGAGCTGGGACTTGAACTCTGGGGATTCTACCTCATTGC-TTTGGTGCTTTGGGTTTGTAATG-----TCTGGTATCTCCACTTCCTCAGATCGATGATAGAGATAAAGATATGATATTAAGGAAGCTGTTAATCCTGAATTTTCAGAAAAGTATCCCTTTATAAAATGTATTTGGGGGG-CAAACTGCATGAGATTATATTCTGGCCCTATAGCTAATCAAAATGTGTTTATTGATTAATCTTTAAAA-GGCTTAATGA-ACAATATTTTAGTCAGATATCTAATTCTTAAATCCTCTAGAAGAATTAACTAAT-CTATAAAATGGGTCTGGATGTAGT-----CTGACATAATTTTATAACAACC-GTAAGAGGGAGTGACTAGAG-CAACAACT----AAAATGATCTCAGG--AAAAACTG--TTTTGGTCCTATGT-ATAGTACATTACATCTTTTCAGTAATTCCATTCAAATGGAGAAGTTTAACAAGGCAACTGTTCTCAGGGGGCCTATTCTCTCCCTTAAAATTCATTATACACATCCCT-GGTTGATAGCAGCGTGTCTGGAGGCAGAAACCATTCTTGCTTTGGAAACAATTATGTCTGTGTTATG--CTGAGTAGGGAAGCTCATTAACTGTCAACACTTATGTT-CCTGATAATGGAATCAATGTGTAATTCTTGTTTTGTTCCAGATTTCTAACACCATAAAGAATAAATCCTTTCACTCT-GATCAATGTTGTTAACTTCTCACCTGT Cheirogaleus GACAAAGTAGAAGTGACTCCTTCCAGTTTTGCCAACCAGCTTTTGTTACTAGGGCAAGGGTACCCAGCATTTA-TTTTTAACATCATTAATTCAAA-------AAGAATGAAGTTCTGC---------AGAGCTTACTGAACCGGGGCTTGGACTCTAGGCACTCTCCTTCATTGC-TTTGGTGCATTAGGTTTGCAATG-----CCTGGCACCTCAATTCCCTCAAATAGATGATAGAAATAAAGATATGATATTCATCAAGCTGTTAATACTGAATTTGCAGAAAAGCATCCCTTTATAAAATTTATTTGAGGGT-AAAACTGCATGAGATTATATTCTGGCCCTTTAGCTAATTAAAATGTATTTATTGATTAATCTGTGAAA-GGCTTGGGGA-ACAACATTCTAGGCAGACATCTAATTCTGAAATCCTCTAGAGGAATTAACTAATACTATAAAATAAGTCAGAAAGTAGT-----CTACTGTTATTTTCCAACAACTAGTAAGAAGGAATTACTACAG-CAACAACTGACTAAAATGATCTCAGG--AAAAACTA---TTTGGTCCTATGTTATGGAACATTACATCTTTTCAGTAATTCCACTCACATGGAGAAGTT-AACAAAGCAACTGTTCTCAGAGGGCCTATTTTCTCCCTCAAAATTCATTATACACGTCCCC-GGTTGATAGCAGCATGACTGGAGGCAGAAACCATTCTTGCTTTGGAAACAATTATGTCTGTGTTGTA--CTGAGTAGGGAAGCTCATTAATTGTCAACACTTACGTT-CCCGGTAATGGGATCAGTGTGTACTCTCTGTTTTGCTCCATATTTCTGACACCATAAAGACTAAATCCTTTCTCACT-GACCAATGTTGTTAACTTCTCACTTGT Colobus_guereza AATGAAGTAGGAGTGACTCCTTCCAGCTTTGCCAACCAGCTTTTGTCACTAGGGCAAGGGTACCCAGCATCTA-TTTTTAATATCATTAATTCAAACTTCAAAAAGAATGAAGTTCCAC---------TGAGCTTACTGAGCTGGGACTTGAACTCTGGGGATTCTGCCTCATTGC-TTTGGTGCACTGGGTCTGTAATG-----TCTGATATCTCCGCTTCCTCAGATCGATGATAGAGATAAAGATGTGATATTAAGGAAGCTGTTAATCCTGAATTTTCAGAAAA-TATCCCTTTATAAAATGTATTTGGGGGG-CAAACTGCATGAGATTATATTCTGGCCCTATAGCTAATCAAAATGTATTTACTGATTAATCTTTAAAA-GGCTTAGTGA-ACAATATTTTAGTCAGATATCTAATTCTTAAATCCTCTAGAAGAATTAACTAAT-CTATACAATGGGTCTGGATGTAGT-----CTGACATAATTTTATAACAACCCGTAAGAGGGGGTGACTAGAG-CAACAACT----AAAATGATCTCAGG--AAACACTG--TTTTGGTCCTGTGT-ATGGTGCATTACCTCTTTTCAGTAATTCCATTCAAATGGAGAAGTTTAACAAGGCAACTGTTCTCAGGGGGCCTATTCTCTCCCTTAAAATTCATTATACACATCCCT-GGTTGATAGCAGCGTGTCTGGAGGCAGAAACCATTCTTGCTTTGGAAACAATTATGTCTGTGTTCTA--CTGAGTAGGGAAGCTCATTAACTGTCAACACT-ATGTT-CCTGATAATGGAATCAGCGTGTAATTCTTGTTTTGTTCCAGATTTCTAACACCATAAAGAATAAATCCTTTCACTCT-GATCAATTTTGTTAACTTCTCACTTGT Daubentonia_madagascariensis GACAAAGTAGAAGTGACTCCTTGC-GTTTTGCCAACCAGCTTTTGTTACTAGGGCAAGGGTACCCA-CATCTAGTTTTAA-CATCATTGATTCAAACCTCAAAAAGAATGAAG--------------------------AACTGGGACTTGGACTCTGGGCACGCTCCTTCATTGC-TTTGGTGCATTGGGTTTGCAATG-----CCTAGCACCTCAATTTCCTCAGATAGATGGCAGGAATAAAGATATGCTATTAATGAAGCTGTTAATATTGCATTTTCAGAAAAGCATCCTTTTATAAAATTTATTTGGGGGT-AAAGCTGCATGAGATTATATCCTGGCCCTTTAGCTAATTCAAATGTATTTACTGAGTAATCTTTGAAA-GGCTTGGTGATGTCTAATTCTAGTCAGATATATAATTCTTAAATCTT-TAGAAGAATTAACTAATACTGTAAAATAAGTCAGAAAGTAGT-----CTAATGTTATTTTACAACAACTAGTAAGAGGGAATTACTACAC-CAACAACTGACTAAAATGATCTCAGG--AAAAACTA---TTTGGTCCTAT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Erythrocebus AATGAAGTAGGAGTGACTCCTTCCAGCTTTGCCAACCAGCTTTTGTTACTAGGGCAAGGGTGCCCAGCATCTA-TTTTTAATATCATTAATTCAAACTTCAAAAAGAATGAAGTTCCAC---------TGAGCTTACTGAGCTGGGACTTGAACTCTGGGGATTCTACCTCATTGC-TTTGGTGCTTTGGGTTTGTAATG-----TCTGGTATCTCCACTTCCTCAGATCGATGATAGAGATAAAGATATGATATTAAGGAAGCTGTTAATCCTGAATTTTCAGAAAAGTATCCCTTTATAAAATGTATTTGGGGGG-CAAACTGCATGAGATTATATTCTGGCCCTATAGCTAATCAAAATGTGTTTATTGATTAATCTTTAAAA-GGCTTAATGA-ACAATATTTTACTCAGATATCTAATTCTTAAATCCTCTAGAAGAATTAACTAAT-CTATAAAATGGGTCTGGATGTAGT-----CTGACATAATTTTATAACAACCGGTAAGAGGGAGTGACTAGAG-CAACAACT----AAAATGATCTCAGG--AAAAACTG--TTTTGGTCCTATGT-ATAGTACATTACATCTTTTCAGTAATTCCATTCAAATGGAGAAGTTTAACAAGGCAACTGTTCTCAGGGGGCCTATTCTCTCCCTTAAAATTCATTATACACATCCCT-GGTTGATAGCAGCGTGTCTGGAGGCAGAAACCATTCTTGCTTTGGAAACAATTATGTCTGTGTTATG--CTGAGTAGGGAAGCTCATTAACTGTCAACACTTATGTT-CCTGATAATGGAATCAATGTGTAATTCTTGTTTTGTTCCAGATTTCTAACACCATAAAGAATAAATCCTTTCACTCT-GATCAATGTTGTTAACTTCTCACTTGT Eulemur_fulvus_albifrons GACAAAGTACAAGTGACTCCTTCCAGTTTTGCCAACCAGCTTTTGTTACTAGGGCAAGGGTACCCAGCATTTA-TTTTTA---TCATTAATTCAAACCTCAAAAAGAAGGCAGTTCTGC---------AGAGCTTACTGAACCGGGGCTTGGGCTCTAGGCACTCTCCTTCATTGC-TTTGGTGCACTGGGTTTGCAATG-----CCTGGTACCTCAATTACCTCAAATAGATGATACAAATAAAGATATGATATTAATTAAGCTGTTAATATTGAATTTTCAGAAAAGCATCCCTTTATAAAATTTATTTCAGGGT-AAAACTGCATGAGATTATATTCTGGCCCTTTAGCTAATGAAAATGTATTTATTGATTCATCTTTGAAA-GGCTTGGGGG-ACAACATTCTAGGCAGACATCTAATTCTTAAATCCTCTAGAAGAATTAACTAATACTATAAAATAAGTCAGAAAGTACT-----CTAATGTTATTTTACAACAACTAGTAAGAGGGAATTACTATAG-CAACAACTGACTAAAATGATCTCAGG--AAAAACTA---TTTGGTCCTATGT-ATGGAACATTACATCTTTTCAGTAATTCCACTCAAATGGAGAAGTT-AACAGAGCAACTGTTCTCAGAGGGCCTATTTTCTCCCTCAAAATTCATTATCCACGTCCCC-GGTCAAA-------TGACTGGAGGCAGAAACCATTCTTGCTTTGGAAACAATTATGTCTGTGTTATA--CTGAGTAGGGAAGCTCATTAATTGTCAACACTTAGGTT-CCCGGTAATGGGATCAGTGTATACTCTCTGTTTTGCTCCAGATTTCTGACACCATAGAGACTAAATCCTTTCCCACT-GACCAATGTTGTTAACTTCTCACTTGT Eulemur_fulvus_collaris GACAAAGTAGACGTGACTCCTTCCAGTTTTGCCAACCAGCTTTTGTTACTAGGGCAAGGGTACCCGGCATTTA-TTTTTA---TCATTAATTCAAACCTCAAAAAGAAGGCAGTTCTGC---------AGAGCTTACTGAACCGGGGCTTGGGCTCTAGGCACTCTCCTTCATTGC-TTTGGTGCACTGGGTTTGCAATG-----CCTGGTACCTCAATTACCTCAAATAGATGATACAAATAAAGATATGATATTAATTAAGCTGTTAATATTGAATTTTCAGAAAAGCATCCCTTTATAAAATTTATTTCAGGGT-AAAACTGCATGAGATTATATTCTGGCCCTTTAGCTAATGAAAATGTATTTATTGATTCATCTTTGAAA-GGCTTGGGGG-ACAACATTCTAGGCAGACATCTAATTCTTAAATCCTCTAGAAGAATTAACTAATACTATAAAATAAGTCAGAAAGTACT-----CTAATGTTATTTTACAACAACTAGTAAGAGGGAATTACTATAG-CAACAACTGACTAAAATGATCTCAGG--AAAAACTA---TTTGGTCCTATGT-ATGGAACATTACATCTTTTCAGTAATTCCACTCAAATGGAGAAGTT-AACAGAGCAACTGTTCTCAGAGGGCCTATTTTCTCCCTCAAAATTCATTATCCACGTCCCC-GGTCAAA-------TGACTGGAGGCAGAAACCATTCTTGCTTTGGAAACAATTATGTCTGTGTTATA--CTGAGTAGGGAAGCTCATTAATTGTCAACACTTAGGTT-CCCGGTAATGGGATCAGTGTATACTCTCTGTTTTGCTCCAGATTTCTGACACCATAGAGACTAAATCCTTTCCCACT-GACCAATGTTGTTAACTTCTCACTTGT Eulemur_fulvus_rufus GACAAAGTAGAAGTGACTCCTTCCAGTTTTGCCAACCAGCTTTTGTTACTAGGGCAAGGGTACCCGGCCTTTA-TTTTTA---TCATTAATTCAAACCTCAAAAAGAAGGCAGTTCTGC---------AGAGCTTACTGAACCGGGGCTTGGGCTCTAGGCACTCTCCTTCATTGC-TTTGGTGCACTGGGTTTGCAATG-----CCTGGTACCTCAATTACCTCAAATAGATGATACAAATAAAGATATGAT-TTAATTAAGCTGTTAATATTGAATTTTCAGAAAAGCATCCCTTTATAAAATTTATTTCAGGGT-AAAACTG-ATGAGATTATATTCTGGCCCTTTAGCTAATGAAAATGTATTTATTGATTCATCTTTGAAA-GGCTTGGGGA-ACAACATTCTAGGCAGACATCTAATTCTTAAATCCTCTAGAAGAATTAACTAATACTATAAAATAAGTCAGAAAGTACT-----CTAATGTTATTTTACAACAACTAGTAAGAGGGAATTACTA-AG-CAACAACTGACTAAAATGATCTCAGG--AAAAACTA---TTTGGTCCTATGT-ATGGAACATTACATCTTTTCAGTAATTCCACTCAAATGGAGAAGTT-AACAGAGCAACTGTTCTCAGAGGGCCTATTTTCTCCCTCAAAATTCATTATCCACGTCCCC-GGTCAAA-------TGACTGGAGGCAGGAACC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Eulemur_macaco_flavifrons GACAAAGTAGAAGTGACTCCTTCCAGTTTTGCCAACCAGCTTTTGTTACTAGGGCAAGGGTACCCGGCATTTA-TTTTTA---TCATTAATTCAAACCTCAAAAAGAAGGCAGTTCTGC---------AGAGCTTACTGAACCGGGGCTTGGGCTCTAGGCACTCTCCTTCATTGC-TTTGGTGCACTGGGTTTGCAATG-----CCTGGTACCTCAATTACCTCAAATAGATGATACAAATAAAGATATCATATTAATTAAGCTGTTAATATTGAATTTTCAGAAAAGCATCCCTTTATAAAATTTATTTCAGGGT-AAAACTGCATGAGATTATATTCTGGCCCTTTAGCTAATGAAAATGTATTTATTGATTCATCTTTGAAA-GGCTTGGGGG-ACAACATTCTAGGCAGACATCTAATTCTTAAATCCTCTAGAAGAATTAACTAATACTATAAAATAAGTCAGGAAGTACT-----CTAATGTTATTTTACAACAACTAGTAAGAGGGAATTACTACAG-CAACAACTGACTAAAATGATCTCAGG--AAAAACTA---TTTGGTCCTATGT-ATGGAACATTACATCTTTTCAGTAATTCCACTCAAATGGAGAAGTT-AACAGAGCAACTCTTCTCAGAGGGCCTATTTTCTCCCTCAAAATTCATTATCCACGTCCCC-GGTCAAA-------TGACTGGAGGCAGAAACCATTCTTGCTTTGGAAACAAT-ATGTCTGTGTTATA--CTGA-TAGGGAAGCTCATTAATTG-CAACACTTATGTT-CCCGG??ATGGGATCAGAGGATACTCTCTG--------------------------------------------------------------------------- Eulemur_macaco_macaco GACAAAGTAGAAGTGACTCCTTCCAGTTTTGCCAACCAGCTTTTGTTACTAGGGCAAGGGTACCCGGCATTTA-TTTTTA---TCATTAATTCAAACCTCAAAAAGAAGGCAGTTCTGC---------AGAGCTTACTGAACCGGGGCTTGGGCTCTAGGCACTCTCCTTCATTGC-TTTGGTGCACTGGGTTTGCAATG-----CCTGGTACCTCAATTACCTCAAATAGATGATACAAATAAAGATATGATATTAATTAAGCTGTTAATATTGAATTTTCAGAAAAGCATCCCTTTATAAAATTTATTTCAGGGT-AAAACTGCATGAGATTATATTCTGGCCCTTTAGCTAATGAAAATGTATTTATTGATTCATCTTTGAAA-GGCTTGGGGG-ACAACATTCTAGGCAGACATCTAATTCTTAAATCCTCTAGAAGAATTAACTAATACTATAAAATAAGTCAGGAAGTACT-----CTAATGTTATTTTACAACAACTAGTAAGAGGGAATTACTACAG-CAACAACTGACTAAAATGATCTCAGG--AAAAACTA---TTTGGTCCTATGT-ATGGAACATTACATCTTTTCAGTAATTCCACTCAAATGGAGAAGTT-AACAGAGCAACTCTTCTCAGAGGGCCTATTTTCTCCCTCAAAATTCATTATCCACGTCCCC-GGTCAAA-------TGACTGGAGGCAGAAACCATTCTTGCTTTGGAAACAATTATGTCTGTGTTATA--CTGAGTAGGGAAGCTCATTAATTGTCAACACTTAGGTT-CCCGGTAATGGGATCAGTGTATACTCTCTGTTTTGCTCCAGATTTCTGACACCATAGAGACTAAATCCTTTCCCACT-GACCAATGTTGTTAACTTCTCACTTGT Felis_silvestris GATGAAGTAGAAGGGCCCTCTCCCAGCTCTGCCAGTCAGCTTGTGTTACTAGGACAAGGGTACCCAGCATCGACTTTTAAATATCATCGATTCAAACTGCAAAATGAATGAAGTTCTGC---------AGAGCTCACTGACCTGGACCTTGGACCCTGGGTGCTCCCCACTATAGC-TTTGGTGCACTGGGTTTACGGTGCCTGGCTCCTTGCCTCAATTTCCTCGAATATATGGTAGGAATAACAATATGATATTCATGAAGCTACCAATATTGCGTTGTCAGATGTGCATCCTTTTATAAAGTTTATTT--------------------------------CCCTTCAGCTCATCAAAATGTATCTATTGATTAATCTCTGAAA-GGCTGGGTGG-ACAACATTCTAGTCGAATACTGAATGCTTAAGTCCTCTAGAGGAATTAACTAATACTATAAAATGCATCCTTAAGTAGTC------GACATTATTTTCCAACCAGTAAGAGGGAATTACTACAACAGCAGCTGACT----AAAACGTTCTCAGG-AAAAACAAGCTATTTGGTCCTGT-----GGCACATTGCATCTTTTTAGTAACTCCACTCAAATGGCAAGGCTTAACAAAGCAACTGTTCTCAGAGGGCCTATTTTCTCCTTTAAAATTCATTATACATGTTCCA-GGTCGATGGCAGCATGTCCGGAGGCAGAAACCAGTCTTTCTTTGGGAACAATCATGTCTGTGTTATATACTGAGAAGGGGAGCTCATTAACTGTCAACACTTACAAT-GCTGGAAATGGACTTGGCATGGACTTCTTGCCTTGTTCCAGATTTCTAACACCATAAAGAACAGCTCCTTTCA-------------------------------- Hapalemur_griseus GACACAGTAGCAGTGACTCCTTCCAGTTTTGCCAACCAGCTTTTGTTACTAGGGCAAGGGTACCCGGCATTTA-TTTTTAACATCATTAATTCAAACCACAAAAAGAATGATGTTCTGC---------AGAGCTTACTGAACCAGGGCTTCGACTCTAGGCACGGTCCTTCATTGC-TTTGGTGCACTGGGTTTGCAATG-----CCTGGTACCTCAATTACCTCAAATAGATGATAGAAATAAAGATATGGTATTTATCAAGCTGTTGACATTGAATTTTCAGAAAAGTATCCCTTTATAAAATTTATTTGGGGGT-AAAACTGCATAAGATTATATTCTGGCCCTTTAGCTAATTAAAATGTATTTATTGATTCATTTTTGAAA-GGCTTGGGGA-AGAACATTCTAGGCAGACATCTAATTCTTAAATCCTCTAGAAGAATTAACTAATACTATAAAATAAGTCAGAAAGTACT-----CTAATGTTATTTTACAACAACTAGTAAGAGGGACTTACTACAG-CAACAACTGACTAAAATGATCTCAGG--AAAAACTA---TTTGGTCCTAGGT-ATGGAACATTACCTCTTTTCAGTAATTCCACTCACATGGAGAAGTT-AACAAAGCAACTGTTCTCAGAGGGCCTATTTTCTCCCTCAAAATTCATTATACACGTCCCC-GGTTGATAATAGCATGACTGGAGGCAGAAACCATTCTTGCTTTGGAAACAATTATGTCTGTGTTGTA--CTGAGTAGGGAAGCTCATTAATTGTCAACACTTATGTT-CCCGGTAATGGGATCAGTGTGTACTCTCTGTTTTGCTCCAGATTTCTGACACCATAAAGACTAAATCCTTTCTCACT-GACCAATGTTGTTAACTTCTCACTTGT Homo_sapiens AATGAAGTAGAAGTGACTCCTTCCAGCTTTGCCAACCAGCTTTTATTACTAGGGCAAGGGTACCCAGCATCTA-TTTTTAATATAATTAATTCAAACTTCAAAAAGAATGAAGTTCCAC---------TGAGCTTACTGAGCTGGGACTTGAACTCTGAGCATTCTACCTCATTGC-TTTGGTGCATTAGGTTTGTAATA-----TCTGGTACCTCTGTTTCCTCAGATAGATGATAGAAATAAAGATATGATATTAAGGAAGCTGTTAATACTGAATTTTCAGAAAAGTATCCCTCCATAAAATGTATTTGGGGGA-CAAACTGCAGGAGATTATATTCTGGCCCTATAGTTATTCAAAACGTATTTATTGATTAATCTTTAAAA-GGCTTAGTGA-ACAATATTCTAGTCAGATATCTAATTCTTAAATCCTCTAGAAGAATTAACTAATACTATAAAATGGGTCTGGATGTAGTT----CTGACATTATTTTATAACAACTGGTAAGAGGGAGTGACTATAG-CAACAACT----AAAATGATCTCAGG--AAAACCTG---TTTGGCCCTATGT-ATGGTACATTACATCTTTTCAGTAATTCCACTCAAATGGAGACTTTTAACAAAGCAACTGTTCTCAGGGGACCTATTTTCTCCCTTAAAATTCATTATACACATCCCT-GGTTGATAGCAGTGTGTCTGGAGGCAGAAACCATTCTTGCTTTGGAAACAATTACGTCTGTGTTATA--CTGAGTAGGGAAGCTCATTAATTGTCGACACTTACGTT-CCTGATAATGGGATCAGTGTGTAATTCTTGTTTCGCTCCAGATTTCTAATACCACAAAGAATAAATCCTTTCACTCT-GATCAATTTTGTTAACTTCTCACGTGT Lemur_catta GACACAATAGCAGTGACTCCTTCCAGTTTTGCCAACCAGCTTTTGTTACTAGGGCAAGGGTACCCGGCATTTA-TTTTTAACATCATTAATTCAAACTACAAAAAGAATGAAGTTCTGC---------AGAGCTTACTGAACCGGGGCTTGGACTCTAGGCTCGGTCCTTCATTGC-TTTGGTGCACTGGGTTTGCAATG-----CCTGGTACCTCAATTACCTCAAATAGATGACAGAAATAAAGATATGGTATTAATCAAGCTGTTGATATTGAATTTTCAGAAAAGTATCCCTTTATAAAATTTATTTGGGGGT-AAAACTGCATAAGATTATATTCTGGCCCTTTAACTAATTAAAACGTATTTATTGATTCATTTTTGAAA-GGCTTGGGGA-AGAACATTCTAGGCAGACATCTAATTCTTAAATCCTCTAGAAGAATTAACTAATACTATAAAATAAGTCAGAAAGTACG-----CTAACGTTATTTTACAACAACTAGTAAGAGGGAATTACTACAG-CAACAACTGACTAAAATGATCTCAGG--AAAAACTA---TTTGGTCCTATGTTATGGAACATTACATCTTTTCAGTAATTCCACTCACATGGAGAAGTT-AACAAAGCAACTGTTCTCAGAGGGCCTATTTTCTCCCTCAAAATTCATTATACACGTCCCC-GGTTGATAGCAGCATGACTGGAGGCAGAAACCATTCTTGCTTTGGAAACAATTATGTCTGTGTTGTA--CTGAGTAGGGAAGCTCATTAATTGTCAACACTTACGTT-CCCGGTAATGGGATCAGTGTGTACTCTCTGTTTTGCTCCATATTTCTGACACCATAAAGACTAAATCCTTTCTCACT-GACCAATGGTGTTAACTTCTCACTTGT Macaca_fuscata AATGAGGTAGGAGTGACTCCTTCCAGCTTTGCCAAGCAGCTTTTGTTACTAGGGCAAGGGTACCCAGCATCTA-TTTTTAATATCATTTATTCAAACTTCAAAAAGAATGAAGTTCCAC---------TGAGCTTACTGAGCTGGGACTTGAACTCTGGGGATTCTGCCTCATTGC-TTTGGTGCATTGGGTTTGTAATG-----TCTGGTATCTCCACTTCCTCAGATCGATGATAGAGATAAAGATATGATATTAAGGAAGCTGTTAATCCTGAATTTTCAGAAAAGTATCCCTTTATAAAATGTATTTGGGGGG-CAAACTGCATGAGATTATATTCTGGCCCTATAGCTAATCAAAATGTGTTTACCGATTAATCTTTAAAA-GGCTTAGTGA-ACAATATTTTAGTCAGATATCTAATTCTTAAATACTCTAGAAGGATTAACTAAT-CTATAAAATGGGTCTGGATATAGT-----CTGACATAATTTTATAACAACCGGTAAGAGGGAGTGACTAGAG-CAACAACT----AAAATC----------------------------------------------------------------------------------------------------------------------------------TACACACAT-CCT-GGTTGATAGCAGTGTGTCTGGAGGCAGAAACCATTCTTGCTTTGGAAACAATTATGTCTGTGTTATA--CTGAATAGGGAAGCTCATTAACTGTCAACACTT-TGTTATTCAATAATGGAATCAGTGTGTAATTC-TGTTT-GTTCCAGATTTCTAACACCATAAAGAATAAATCCTTTCACTCT-GATCAATGTTGTTAACTTCTCACTTGT Saguinus_sp. CCTGAAGTAGAAGTAGCTCCTTCCGGCTTTGCCAACCAGCTTTTGTTACTAGGGCAAGGGTACTCAGCATCTG-TTTTAAATATCATTGATT-GAACTTCAAAAAGAATGAAGCTCCGCTGAGCTTGCTGAGCTTACTGAGCTGGGACTTGAATTCTAGACATTCTGCCTCATAGC-TTCGGTGTACTGGGTTTGCAAAG-----TCTGGTACCTCAATTTCCTCAGATAGATGATAGAAATAAAGATGTGATATTAAGGAAGCTGTTAATACTGAATTTTCAGAAAAGCGTCCCTTTATCAAATGTATTTGGGGGG-CAAACCGCATGAGATTATATTCTGGCCCTATAGCTAGTCAAAATGTATTTATTGATTAATCTTTAAAA-GGCT-GGTGA-GCAATATTCTAGATATCTATCTAATTCTTAAATCCTCTAGAAGAATTAATTAATACTATAAAATGGGTCAGGATGTAGA-----CTGATGTTATTTTATAACAACCGGTAAGAGGGAGCGACTATGG-CAACAACT----AAAATGATCTCAGG--GAAAACTC---TTTGGCCCTATGT-ATGATACATTACATCTTTTCAGTAATTCCACTCAAATGGAGAGGCTTAACAAAGCAACTATCCTCAGGGGGCCAATTTTCTCCCTTAAAATTCATTATACGCATCCCCTGGTTGATAGCGGCATGTCTGGAGGCAGAAACCATTCTTGCTTTGGAAATAATTATGTCTGTGTTATA--CTGCATAGGGAAGCTCAGTAATTGTCAACACTTTTGTT-CCTGATAATGGGATCAGTGTGTAATTCTTGCTTTGTTCCAGATTTCTAATACCATGAACCATAAATCCTTCCACTCT-GATCAATTTTGTTAACTTCTCATTTGT Scalopus_aquaticus G-CGAAGTAGAAGTGGCTTCTTCCAGCTTTGCCAACCAGCCTTTGTTCCTAGGGCAAGGGGGCTCACCATCTCTTCTGAAACATCATTGATTCAAATTCCAAAAAGAATGAAGCTTTGC---------TCAGCTCACTGAACTGGGGCTTGGATTCTGGGTGCTTTCGCCTTTTGTTTTTGGTGTTTTGGGTTCACTATG-----CTCGGCACCTCAATTTCCTGAGATAGATGGTAGAAATAATGATATGCTATTTGTGAAGCTATTTATAGAGAATTTTCATAAATGTATACCTTTATAAAATTTATTT--------------------------------CCCTTTAGCTAATCAAAATGAATTTATCGACTATTCTTTGAAA-GGCTTAGAGG-GCACTATTTGATATCTTAAGTACTCTAGAAGAGTTTAATAAACACTATACAATGGATCTTGAAGTCATGCAACATCATTTTACAACAACATTATTTTACAACAACTAAGAAGGAATTGATTATTTGGGCAATAACTGACTAAAATGCTCTCAGG--AAAAT----GATTTGGTTCCAT-----GGAATGTTATATATTTTCAATAATTCCACTCAAACAGCAAGGCTTAATGAAGCCACTGGTCTCAGG-AGCCTATTCTCTCCTTTAAAATTCATTGTATATGTCCCC-AGTTGAGCTCAGTGTGTCTGGAGGCGAAAACCATTCTTGCTTTGGGAACACTCTTGTCTGTGTTATA--CTGCGTAGGGAAGCTCGTTGACTGTCAACAGTTCAGTT-GCAGGAAATGCGATTAGAATATACTTCCTGCCTTGTTCCAGATTTCTAGTATCATAATGAGTGGACCCTTTAT-------------------------------- Varecia_variegata_rubra GACAAAGTAGCAGTGACTGCTTCCAGTTTTGCCAACCAGCTTTTGTTACTAGGGCAAGGGTACCCAGCATTTA-TTTTTAACATCATTAATTCACACCTCAAAAAGAATGAAGTTCTGC---------AGAGCCTACTGAACCGGGGCTGGAACTCTAGGCACTCTCATTCATTGC-TTTGGTGCATTAGGTTTGCAATG-----CCTGGTACCTCAATTACCTCAAATAGATGATAGAAATAAAGATATGGTATTCATTAAGCTGTTAATATTGAATTTGCAGAAAAGCATCCCTTTATAAAATTTATTTGTGGGT-AAAACTGCATGAGATTATATTCTGGCCCTTTAGCTAATTAAAATGTATTTATTGATTCATCTTTGAAA-GGCTTGGGGA-ACAACATTCTAGGCAGACATCTAATTCTTAAATCCTCTGGAAGAATTAACTAATACTATAAAATAAGATAGAAAGTACT-----CTAATGTTATTTTACAACAGCTAGTAAGAGGGAATTGCTACAG-CAACAACTGACTAAAATGATCTCAGG--AAAAACTA---TTTGGTCCTATGT-ATGAAACATGAT-T-TTTTCAGTAATTCCACTCACATGGAGAA-TTTAACAAAGCAAATGTTCTCAGAGGGCCTATTTTCTCCCTCAAAATTCATTATACACGTCCCC-AGTGGATA-CAGCATGACTGGAGGCAGAAATCATTCTTGCTTTGGAAACAATTATGTCTGTGTTATA--CTGAGTAGGGAAGCTCA-TAA-TG-CAACACTTATGTT-CCCAGTAATGGGATCAGTGTATACTCTCTGTTTTGCTCCAGATTTCTGACACCATAAAGACTAAATCCTTTCCCACT-GACCAAC-TTGTTAACTTCTCACTTGT Varecia_variegata_variegata GACAAAGTAGCAGTGACTGCTTCCAGTTTTGCCAACCAGCTTTTGTTACTAGGGCAAGGGTACCCAGCATTTA-TTTTTAACATCATTAATTCACACCTCAAAAAGAATGAAGTTCTGC---------AGAGCCTACTGAACCGGGGCTGGAACTCTAGGCACTCTCATTCATTGC-TTTGGTGCATTAGGTTTGCAATG-----CCTGGTACCTCAATTACCTCAAATAGATGATAGAAATAAAGATATGGTATTCATTAAGCTGTTAATATTGAATTTGCAGAAAAGCATCCCTTTATAAAATTTATTTGTGGGT-AAAACTGCATGAGATTATATTCTGGCCCTTTAGCTAATTAAAATGTATTTATTGATTCATCTTTGAAA-GGCTTGGGGA-ACAACATTCTAGGCAGACATCTAATTCTTAAATCCTCTGGAAGAATTAACTAATACTATAAAATAAGATAGAAAGTACT-----CTAATGTTATTTTACAACAGCTAGTAAGAGGGAATTGCTACAG-CAACAACTGACTAAAATGATCTCAGG--AAAAAC-A---TTTGGTCCTATGT-A?GAAACAT-ATATTTTTTCAGTAATTCCACTCACATGGAGAAGTT-AACAAAGCAA-TGTTCTCAGAGGGCCTATTTTCTCCCTCAAAATTCATTATACACGTCCCC-AGTGGATA-CAGCATGACTGGAGGCAGAAATCATTCTTGCTTTGGAAACAATTATGTCTGTGTTATA--CTGAGTAGGGAAGCTCA-TAA-TGTCAACACTTATGTT-CC??GTAATGGGATCAGTGTATACTCTCTGTTTTGCTCCAGATTTCTGACACCATAAAGACTAAATCCTTTCCCACT-GACCAAC-TTGTTAACTTCTCACTTGT ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = 'Transthyretin (intron 1)') = N: 1-901; CODONPOSSET CodonPositions (CHARACTERS = 'Transthyretin (intron 1)') = N: 1-901; END; [ The following blocks are output data for analysis step 2087 ] BEGIN TREES; TITLE Tb6862; LINK TAXA = TaxaForAnalysisStep2087; TREE TR_usertree = [&R] (((((Cheirogaleus,(((((Eulemur_fulvus_albifrons,Eulemur_fulvus_rufus),Eulemur_fulvus_collaris),(Eulemur_macaco_macaco,Eulemur_macaco_flavifrons)),(Lemur_catta,Hapalemur_griseus)),(Varecia_variegata_rubra,Varecia_variegata_variegata))),Daubentonia_madagascariensis),((Callithrix_jacchus,Saguinus_sp.),((Colobus_guereza,(Macaca_fuscata,(Cercopithecus,Erythrocebus))),Homo_sapiens))),(Canis_lupus,Felis_silvestris)),Scalopus_aquaticus); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr1782] END;