#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 16, 2026; 13:15 GMT TreeBASE (cc) 1994-2008 Study reference: Lagreca S., & Lumbsch H. 2001. No evidence from rDNA ITS sequence data for a placement of Ramalinora in the Ramalinaceae. The Lichenologist, 33(2): 172-176. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S698] [ The following blocks are input data for analysis step 1060 ] BEGIN TAXA; TITLE TaxaForAnalysisStep1060; DIMENSIONS NTAX=13; TAXLABELS Lecanora_contractula Lecanora_garovaglii Lecanora_glabrata Lecanora_muralis Lecanora_polytropa Lecanora_varia Ramalina_fraxinea Ramalina_intermedia Ramalina_leptocarpha Ramalina_menziesii Ramalina_montagnei Ramalina_sinensis Ramalinora_glaucolivida ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2644] TITLE Alignment_2; LINK TAXA = TaxaForAnalysisStep1060; DIMENSIONS NCHAR=365; 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 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Lecanora_contractula AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGC-ACCCCTCAAGC-TCTGCTTGGTATTGGGCC--T-CGC-CC---------CCGCGG------GTGG-ACCCGAAAGTCAGTGGCGGCCC--GGCGCGACTTCGAGCGTAGTAAA-TCAT--CTCCCGC-TTTGGAAGT-TGGCGTC--CAG-G-CC-GGCCAGC---CA-----GCCTTTTTATT-TTCAAT--GATTGACC Lecanora_garovaglii AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTACCACC-CTCAAGC-TCAGCTTGGTATTGGGAC--TTCGC-C------TT--CCGAG-------GCGT-GCCCGAAAGTCAGTGGCGGCCC--GGCGTGACTTCGAGCGTAGTAAA-TT-T-TCTCCCGC-TTTGGAAGCC-CGCGTC----GTGACC-GGCCAGA--ACG------CCCAAAACTTTTTCAAT--GATTGACC Lecanora_glabrata AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGC-ACCCCTCAAGC-TCTGCTTGGTATTGGGCC-CT-CGC-CC---------CCGCG-------GCGT-GCCCGAAAATCAGTGGCGGCCC--GGCGAGACTTCGAGCGTAGTAAA-TG-T-TCTCCCGC-TTTGGAAGC-TCCCG-CTGC-G--GCCCG-CCAGA--ACC------CCACAAACTT-TTCACAATGATTGACC Lecanora_muralis -AAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTAC-ACCCCTCAAGC-TCCGCTTGGTATTGGGTC--TTCGCTCT---------TCG-GA------GCGG-GCCCGAAAGTTAGTGGCGGCCC--GGCGTGACTTCGAGCGTAGTAA--TCTT-TCTCCCGC-TCTGGAAGC-TCGCG-C--C-GTGACC-GGCCAGA--AC------GCCCCAAT-TT-TTCAAT--GATTGACC Lecanora_polytropa AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGC-ACCCCTCAAGCGT-AGCTTGGTATTGGGCC--TCCGC-CC---------CCGCG-------GCGG-GCCTGAAAGTCAGTGGCGGTCC--AGTGTGACTTCAAGCGTAGTAAAATA---CCTCCCGC-TTTGGAAGC-TCGCG-A--C-GTGGCC-GGCCAGA--ACG-------CCCA-ACTT-TTCAAT--GATTGACC Lecanora_varia AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAAAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTACCACC-CTCAAGC-TCAGCTTGGTATTGGGAC--TTCGC-C------TT--CCGAG-------GCGT-GCCCGAAAGTCAGTGGCGGCCC--GGCGTGACTTCGAGCGTATTAAA-TT-T-TCTCCCGC-TTTGGAAGCC-CGCG-T--C-GTGACC-GGCCAGA--ACG------CCCAAAACTTTTTCAAT--GATTGACC Ramalina_fraxinea AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCT-GTTCGAGCAGTCATTGC-ACCACTCAAGCGTA-GCTTGGTATTGGGTC-CTTCGC-CCGGGG-TCTCCCGCG-------GCGG-GCCCGAAAAGCATTGGCGGTCC--GGCGTGACTTTAAGCGTAGTAAA-TT-T-TCTCCCGC-TTTGAAAGCCTCGCG-C--C-G--GCCCGGCCAGACAACC------CCCCAATCTT-T-CAC---GATTGACC Ramalina_intermedia AAAACTTTCAACAACGGATCTCTTGGTTCTGGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGC-ACCATTCAAGCGT-AGCTTGGTATTGGGTC-CTTCGC-CGGGGG-TACTCCCCG-------G-GGTGCCCGAAAAGCATTG-CGGTCC--GGTGTGACT-TAAGCGTAGTAAA-TC-T-TCTCCCGC-TTTGAAAGCCTCGCA-C--C-GTGGCC-GGCCAGACAACC-----C--CCATA-TTTCTCAC---GATCGACC Ramalina_leptocarpha AAAACTTTCAACAACGGATCTCTTGGTTCCAG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTAC-ATCATTCAAGCGT-AGCTTGGCATTGGGTCACT-CGC-CCAAA---AC-CATTG-------GCGG-GCCCGAAAACCATTGGCAGTCC--GGCGTGACTTTGAGCGTAGTAAA-T--T-TCTCCCGC-TTTGAAAGCCTCGCG-C--C-GA--CCTGGCCAGATAAA-----------ATA-AT---CAC---GATTGACC Ramalina_menziesii AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTAC-ATCATTCAAGCGT-AGCTTGGCATTGGGTC-ATTCGC-CCGGGG-TG--------------GCGG-GCCCGAAAACCATTGGCGGTTC--GGTGTGACTTTAAGCGTAGTAAA-T--T-TCTCCCGC-TTTGAAAGCCTCGCG-C--C-G--GCC-CGCCAGACAACCGAGAAACCCGATT-AT-CTCAC---GATTGACC Ramalina_montagnei AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGC-ACCATTCAAGCGT-AGCTTGGTATTGGGTT-TTTCGC-CGGGGGCTTTTCCCCA-------GCGT-GCCCGAAAAGCATTGGCGGTCC--GGTGCGACTTTAAGCGTAGTAAA-TA-T-TCTCCCGC-TTTGAAAGCCTCGTG-C--T-GTGGCC-GGCCAGACAACC-----CCCCCAT--AT-CTCAC---GATTGACC Ramalina_sinensis AAAACTTTCAACAACGGATCTCTTGGTTCTG--CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGC-ACCACTCAAGCGT-AGCTTGGTATTGGGTT-CTTCGC-CCGGGG-TCTCCCGCG-------GCGT-GCCCGAAAAGCATTGGCGGTCC--GGAGCGACTTTAAGCGTAGTAAA-TTTT-TCTCCCGC-TTCGAAAGCCTCGCC-C--C-GGGTCC-GGCCAGACAACC-----CCCACATATAT-CTCAC---GATTGACC Ramalinora_glaucolivida AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATC-ATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCTCCTCGGTATTCCGGGGAGCATGCCTG-TTCGAGC-GTCATTACAACC-CTCAAGCGTAAGCTTGGTATTGGGTC--TTCGC-C-G----TCCCCCTCGGGGGGTGGCGG-GCCCGAAAGACAGTGGCGGTCCCCGG-G-GATTTCGCGCGTAGTAAAATTCTATCTCCCGCGTTGGAAAGA-AC-CGTTT---GGAGCC-GGCCAGACAAC-----------AAAAAT-TTCTAT--GATT---- ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = Alignment_2) = N: 1-365; CODONPOSSET CodonPositions (CHARACTERS = Alignment_2) = N: 1-365; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M3674] TITLE Alignment_4; LINK TAXA = TaxaForAnalysisStep1060; DIMENSIONS NCHAR=350; 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] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .] Lecanora_contractula AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGCACCCCTCAAGCTCT-GCTTGGTATTGGGCC-T-CGC-C-------C-CCGCGG-GTGGACCCGAAAGTCAGTGGCGGCCCGGCGCGACTTCGAGCGTAGTAAA-TCAT--CTCCCGC-TTTGGAAGT--TGGCGTCCAGGCCGGCCAGCCAGCC-------TTTTTA-TT-TTCAAT--GATTGACC Lecanora_garovaglii AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTACCACCCTCAAGCTCA-GCTTGGTATTGGGAC-TTCGCC--------TTCCGAG--GCGTGCCCGAAAGTCAGTGGCGGCCCGGCGTGACTTCGAGCGTAGTAAA-TT-T-TCTCCCGC-TTTGGAAGC-C-CGCGTCGTGACCGGCCAG--AACG------CCCAAAACTTTTTCAAT--GATTGACC Lecanora_glabrata AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGCACCCCTCAAGCTCT-GCTTGGTATTGGGCCCT-CGCCC---------CCGCG--GCGTGCCCGAAAATCAGTGGCGGCCCGGCGAGACTTCGAGCGTAGTAAA-TG-T-TCTCCCGC-TTTGGAAGCTCCCGCTGCG-GCCCG-CCAGA--ACC------CCACAAACTT-TTCACAATGATTGACC Lecanora_muralis -AAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTACACCCCTCAAGCTCC-GCTTGGTATTGGGTC-TTCGCTC-------T-TCG-GA-GCGGGCCCGAAAGTTAGTGGCGGCCCGGCGTGACTTCGAGCGTAGTAA--TCTT-TCTCCCGC-TCTGGAAGC--TCGCGCCGTGACCGGCCAGAACGCC-------CCAAT--TT-TTCAAT--GATTGACC Lecanora_polytropa AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGCACCCCTCAAGCGTA-GCTTGGTATTGGGCC-TCCGCCC---------CCGCG--GCGGGCCTGAAAGTCAGTGGCGGTCCAGTGTGACTTCAAGCGTAGTAAA-AT-A-CCTCCCGC-TTTGGAAGC--TCGCGACGTGGCCGGCCAG--AACG-------CCCAACTTT--TCAAT--GATTGACC Lecanora_varia AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAAAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTACCACCCTCAAGCTCA-GCTTGGTATTGGGAC-TTCGCC--------TTCCGAG--GCGTGCCCGAAAGTCAGTGGCGGCCCGGCGTGACTTCGAGCGTATTAAA-TT-T-TCTCCCGC-TTTGGAAGC-C-CGCGTCGTGACCGGCCAG--AACG------CCCAAAACTTTTTCAAT--GATTGACC Ramalina_fraxinea AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCT-GTTCGAGCAGTCATTGCACCACTCAAGCGTA-GCTTGGTATTGGGTCCTTCGCCCGGGG-TCTCCCGCG--GCGGGCCCGAAAAGCATTGGCGGTCCGGCGTGACTTTAAGCGTAGTAAA-TT-T-TCTCCCGC-TTTGAAAGC-CTCGCGCCG-GCCCGGCCAGACAACC------CCCCAATCTT-T-CAC---GATTGACC Ramalina_intermedia AAAACTTTCAACAACGGATCTCTTGGTTCTGGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGCACCATTCAAGCGTA-GCTTGGTATTGGGTCCTTCGCCGGGGG-TACTCCCCG--GGGTGCCCGAAAAGCATTG-CGGTCCGGTGTGACT-TAAGCGTAGTAAA-TC-T-TCTCCCGC-TTTGAAAGC-CTCGCACCGTGGCCGGCCAGACAACC-----C--CCATA-TTTCTCAC---GATCGACC Ramalina_leptocarpha AAAACTTTCAACAACGGATCTCTTGGTTCCAG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTACATCATTCAAGCGTA-GCTTGGCATTGGGTCACTCGCCCAAA---AC-CATTG--GCGGGCCCGAAAACCATTGGCAGTCCGGCGTGACTTTGAGCGTAGTAAA-T--T-TCTCCCGC-TTTGAAAGC-CTCGCGCCGAC-CTGGCCAGATAAA-----------ATA-AT---CAC---GATTGACC Ramalina_menziesii AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTACATCATTCAAGCGTA-GCTTGGCATTGGGTCATTCGCCCGGGG-TG---------GCGGGCCCGAAAACCATTGGCGGTTCGGTGTGACTTTAAGCGTAGTAAA-T--T-TCTCCCGC-TTTGAAAGC-CTCGCGCCG--GCCCGCCAGACAACCGAGAAACCCGATT-AT-CTCAC---GATTGACC Ramalina_montagnei AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGCACCATTCAAGCGTA-GCTTGGTATTGGGTTTTTCGCCGGGGGCTTTTCCCCA--GCGTGCCCGAAAAGCATTGGCGGTCCGGTGCGACTTTAAGCGTAGTAAA-TA-T-TCTCCCGC-TTTGAAAGC-CTCGTGCTGTGGCCGGCCAGACAACC-----CCCCCAT--AT-CTCAC---GATTGACC Ramalina_sinensis AAAACTTTCAACAACGGATCTCTTGGTTCTG--CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGCACCACTCAAGCGTA-GCTTGGTATTGGGTTCTTCGCCCGGGG-TCTCCCGCG--GCGTGCCCGAAAAGCATTGGCGGTCCGGAGCGACTTTAAGCGTAGTAAA-TTTT-TCTCCCGC-TTCGAAAGC-CTCGCCCCGGGTCCGGCCAGACAACC-----CCCACATATAT-CTCAC---GATTGACC Ramalinora_glaucolivida AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATC-ATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCTCCTCGGTATTCCGGGGAGCATGCCTG-TTCGAGC-GTCATTACAACCCTCAAGCGTAAGCTTGGTATTGGGTC-TTCGCCGTCCCCCTCGGGGGGTGGCGGGCCCGAAAGACAGTGGCGGTCCCCGGGGATTTCGCGCGTAGTAAAATTCTATCTCCCGCGTTGGAAAGAAC-CGTTTGGAG-CCGGCCAGACAAC----------AAAAATT--TCTAT--GATT---- ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = Alignment_4) = N: 1-350; CODONPOSSET CodonPositions (CHARACTERS = Alignment_4) = N: 1-350; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2695] TITLE Alignment_1; LINK TAXA = TaxaForAnalysisStep1060; DIMENSIONS NCHAR=365; 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 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Lecanora_contractula AAAA-CTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGC-ACCCCTCAAGC-TCT-GCTTGGTATTGGG-C-CT-CGC---CC-----C---CGCG-GGTGG-ACCCGAAAGTCAGTGGCGGCCC--GGCGCGACTTCGAGCGTAGTAAA-TCAT--CTCCCGC-TTTGGAAGT-TGGCGTC--CAG--G-CC-GGCCAGC---CA----GCCTTTTTA-TTT-T-CAA--TGATTGACC Lecanora_garovaglii AAAA-CTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTACCACCC-TCAAGC-TCA-GCTTGGTATTGGG-A-CTTCGC---CT-----T---CC-GAGGCGT-GCCCGAAAGTCAGTGGCGGCCC--GGCGTGACTTCGAGCGTAGTAAA-TT-T-TCTCCCGC-TTTGGAAGCC-CGCG-T--C-GT-GACC-GGCCAGA--ACG-----CCCA-AAACTTT-TTCAA--TGATTGACC Lecanora_glabrata AAAA-CTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGC-ACCCCTCAAGC-T-CTGCTTGGTATTGGGCC-CT-CGC---CC----------CCGCGGCGT-GCCCGAAAATCAGTGGCGGCCC--GGCGAGACTTCGAGCGTAGTAAA-TG-T-TCTCCCGC-TTTGGAAGC-TCCCG-CTGC-G--GCCC-G-CCAGA--ACC-----CCACAAA-CTT--TTCACAATGATTGACC Lecanora_muralis -AAA-CTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTAC-ACCCCTCAAGC-TCC-GCTTGGTATTGGG-T-CTTCGCT--CT-----T---CG-G-AGCGG-GCCCGAAAGTTAGTGGCGGCCC--GGCGTGACTTCGAGCGTAGTAA--TCTT-TCTCCCGC-TCTGGAAGC-TCGCG-C--C-GT-GACC-GGCCAGA--AC-----GCCCCAAT--TTT-T-CAA--TGATTGACC Lecanora_polytropa AAAA-CTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGC-ACCCCTCAAGCGT-A-GCTTGGTATTGGG-C-CTCCGC---CC---------CC-GCGGCGG-GCCTGAAAGTCAGTGGCGGTCC--AGTGTGACTTCAAGCGTAGTAAA-AT-A-CCTCCCGC-TTTGGAAGCT-CGCG-A--C-GT-GGCC-GGCCAGA--ACG-----CCCA-A--CTTT-T-CAA--TGATTGACC Lecanora_varia AAAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAAAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTACCACCC-TCAAGC-TCA-GCTTGGTATTGGG-A-CTTCGC---CT-----T---CC-GAGGCGT-GCCCGAAAGTCAGTGGCGGCCC--GGCGTGACTTCGAGCGTATTAAA-TT-T-TCTCCCGC-TTTGGAAGCC-CGCG-T--C-GT-GACC-GGCCAGA--ACG-----CCCA-AAACTTT-TTCAA--TGATTGACC Ramalina_fraxinea AAAA-CTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCT-GTTCGAGCAGTCATTGC-ACCACTCAAGCGT-A-GCTTGGTATTGGGTC-CTTCGC---CCGGGG-T-CTCCCGCGGCGG-GCCCGAAAAGCATTGGCGGTCC--GGCGTGACTTTAAGCGTAGTAAA-TT-T-TCTCCCGC-TTTGAAAGCCTCGCG-C--C-G--GCCC-GGCCAGACAACC-----CCCCAAT-CTT--T-CAC---GATTGACC Ramalina_intermedia AAAA-CTTTCAACAACGGATCTCTTGGTTCTGGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGC-ACCATTCAAGCGT-A-GCTTGGTATTGGGTC-CTTCGC---CGGGGG-TACTCCC-CGG-GGTGCCCGAAAAGCATTG-CGGTCC--GGTGTGACT-TAAGCGTAGTAAA-TC-T-TCTCCCGC-TTTGAAAGCCTCGCA-C--C-GTGG-CC-GGCCAGACAACC-----C-CC-ATA-TTTCT-CAC---GATCGACC Ramalina_leptocarpha AAAA-CTTTCAACAACGGATCTCTTGGTTCCAG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTAC-ATCATTCAAGCGT-A-GCTTGGCATTGGGTCACT-CGC---CCAAA---AC-CAT-TGGCGG-GCCCGAAAACCATTGGCAGTCC--GGCGTGACTTTGAGCGTAGTAAA-T--T-TCTCCCGC-TTTGAAAGCCTCGCG-C--C-GA---CCTGGCCAGATAAA-----------ATA-AT----CAC---GATTGACC Ramalina_menziesii AAAA-CTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTAC-ATCATTCAAGCGT-A-GCTTGGCATTGGGTC-ATTCGC---CCGGGG-TG--------GCGG-GCCCGAAAACCATTGGCGGTTC--GGTGTGACTTTAAGCGTAGTAAA-T--T-TCTCCCGC-TTTGAAAGCCTCGCG-C--C-G--G-CC-CGCCAGACAACCGAGAAACCCGATT-AT-CT-CAC---GATTGACC Ramalina_montagnei AAAA-CTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGC-ACCATTCAAGCGT-A-GCTTGGTATTGGGTT-TTTCGC---CGGGGGCTTTTCCC-CAGCGT-GCCCGAAAAGCATTGGCGGTCC--GGTGCGACTTTAAGCGTAGTAAA-TA-T-TCTCCCGC-TTTGAAAGCCTCGTG-C--T-GTGG-CC-GGCCAGACAACC-----CCCCCAT--AT-CT-CAC---GATTGACC Ramalina_sinensis AAAA-CTTTCAACAACGGATCTCTTGGTTCTG--CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGC-ACCACTCAAGCGT-A-GCTTGGTATTGGGTT-CTTCGC---CCGGGG-T-CTCCCGCGGCGT-GCCCGAAAAGCATTGGCGGTCC--GGAGCGACTTTAAGCGTAGTAAA-TTTT-TCTCCCGC-TTCGAAAGCCTCGCC-C--C-G-GGTCC-GGCCAGACAACC-----CCCACATATAT-CT-CAC---GATTGACC Ramalinora_glaucolivida AAAA-CTTTCAACAACGGATCTCTTGGTTCTGG-CATC-ATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCTCCTCGGTATTCCGGGGAGCATGCCTG-TTCGAGC-GTCATTACAACCC-TCAAGCGTAA-GCTTGGTATTGGG-T-CTTCGCCGTCCC--CCTCGGGGGGTGGCGG-GCCCGAAAGACAGTGGCGGTCCCCGG-G-GATTTCGCGCGTAGTAAAATTCTATCTCCCGCGTTGGAAAGAA-C-CGTT--TGGA-G-CC-GGCCAGACAAC---------AAAAA-TT--T-CTA--TGATT---- ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = Alignment_1) = N: 1-365; CODONPOSSET CodonPositions (CHARACTERS = Alignment_1) = N: 1-365; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2597] TITLE Alignment_3; LINK TAXA = TaxaForAnalysisStep1060; DIMENSIONS NCHAR=350; 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] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .] Lecanora_contractula AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGCACCCCTCAAGCTCT-GCTTGGTATTGGGCC-T-CGC-C-------C-CCGCGG-GTGGACCCGAAAGTCAGTGGCGGCCCGGCGCGACTTCGAGCGTAGTAAA-TCAT--CTCCCGC-TTTGGAAGT--TGGCGTCCAGGCCGGCCAGCCAGCC-------TTTTTA-TT-TTCAAT--GATTGACC Lecanora_garovaglii AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTACCACCCTCAAGCTCA-GCTTGGTATTGGGAC-TTCGCC--------TTCCGAG--GCGTGCCCGAAAGTCAGTGGCGGCCCGGCGTGACTTCGAGCGTAGTAAA-TT-T-TCTCCCGC-TTTGGAAGC-C-CGCGTCGTGACCGGCCAG--AACG------CCCAAAACTTTTTCAAT--GATTGACC Lecanora_glabrata AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGCACCCCTCAAGCTCT-GCTTGGTATTGGGCCCT-CGCCC---------CCGCG--GCGTGCCCGAAAATCAGTGGCGGCCCGGCGAGACTTCGAGCGTAGTAAA-TG-T-TCTCCCGC-TTTGGAAGCTCCCGCTGCG-GCCCG-CCAGA--ACC------CCACAAACTT-TTCACAATGATTGACC Lecanora_muralis -AAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTACACCCCTCAAGCTCC-GCTTGGTATTGGGTC-TTCGCTC-------T-TCG-GA-GCGGGCCCGAAAGTTAGTGGCGGCCCGGCGTGACTTCGAGCGTAGTAA--TCTT-TCTCCCGC-TCTGGAAGC--TCGCGCCGTGACCGGCCAGAACGCC-------CCAAT--TT-TTCAAT--GATTGACC Lecanora_polytropa AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGCACCCCTCAAGCGTA-GCTTGGTATTGGGCC-TCCGCCC---------CCGCG--GCGGGCCTGAAAGTCAGTGGCGGTCCAGTGTGACTTCAAGCGTAGTAAA-AT-A-CCTCCCGC-TTTGGAAGC--TCGCGACGTGGCCGGCCAG--AACG-------CCCAACTTT--TCAAT--GATTGACC Lecanora_varia AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAAAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTACCACCCTCAAGCTCA-GCTTGGTATTGGGAC-TTCGCC--------TTCCGAG--GCGTGCCCGAAAGTCAGTGGCGGCCCGGCGTGACTTCGAGCGTATTAAA-TT-T-TCTCCCGC-TTTGGAAGC-C-CGCGTCGTGACCGGCCAG--AACG------CCCAAAACTTTTTCAAT--GATTGACC Ramalina_fraxinea AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCT-GTTCGAGCAGTCATTGCACCACTCAAGCGTA-GCTTGGTATTGGGTCCTTCGCCCGGGG-TCTCCCGCG--GCGGGCCCGAAAAGCATTGGCGGTCCGGCGTGACTTTAAGCGTAGTAAA-TT-T-TCTCCCGC-TTTGAAAGC-CTCGCGCCG-GCCCGGCCAGACAACC------CCCCAATCTT-T-CAC---GATTGACC Ramalina_intermedia AAAACTTTCAACAACGGATCTCTTGGTTCTGGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGCACCATTCAAGCGTA-GCTTGGTATTGGGTCCTTCGCCGGGGG-TACTCCCCG--GGGTGCCCGAAAAGCATTG-CGGTCCGGTGTGACT-TAAGCGTAGTAAA-TC-T-TCTCCCGC-TTTGAAAGC-CTCGCACCGTGGCCGGCCAGACAACC-----C--CCATA-TTTCTCAC---GATCGACC Ramalina_leptocarpha AAAACTTTCAACAACGGATCTCTTGGTTCCAG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTACATCATTCAAGCGTA-GCTTGGCATTGGGTCACTCGCCCAAA---AC-CATTG--GCGGGCCCGAAAACCATTGGCAGTCCGGCGTGACTTTGAGCGTAGTAAA-T--T-TCTCCCGC-TTTGAAAGC-CTCGCGCCGAC-CTGGCCAGATAAA-----------ATA-AT---CAC---GATTGACC Ramalina_menziesii AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTACATCATTCAAGCGTA-GCTTGGCATTGGGTCATTCGCCCGGGG-TG---------GCGGGCCCGAAAACCATTGGCGGTTCGGTGTGACTTTAAGCGTAGTAAA-T--T-TCTCCCGC-TTTGAAAGC-CTCGCGCCG--GCCCGCCAGACAACCGAGAAACCCGATT-AT-CTCAC---GATTGACC Ramalina_montagnei AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGCACCATTCAAGCGTA-GCTTGGTATTGGGTTTTTCGCCGGGGGCTTTTCCCCA--GCGTGCCCGAAAAGCATTGGCGGTCCGGTGCGACTTTAAGCGTAGTAAA-TA-T-TCTCCCGC-TTTGAAAGC-CTCGTGCTGTGGCCGGCCAGACAACC-----CCCCCAT--AT-CTCAC---GATTGACC Ramalina_sinensis AAAACTTTCAACAACGGATCTCTTGGTTCTG--CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTG-TTCGAGC-GTCATTGCACCACTCAAGCGTA-GCTTGGTATTGGGTTCTTCGCCCGGGG-TCTCCCGCG--GCGTGCCCGAAAAGCATTGGCGGTCCGGAGCGACTTTAAGCGTAGTAAA-TTTT-TCTCCCGC-TTCGAAAGC-CTCGCCCCGGGTCCGGCCAGACAACC-----CCCACATATAT-CTCAC---GATTGACC Ramalinora_glaucolivida AAAACTTTCAACAACGGATCTCTTGGTTCTGG-CATC-ATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCTCCTCGGTATTCCGGGGAGCATGCCTG-TTCGAGC-GTCATTACAACCCTCAAGCGTAAGCTTGGTATTGGGTC-TTCGCCGTCCCCCTCGGGGGGTGGCGGGCCCGAAAGACAGTGGCGGTCCCCGGGGATTTCGCGCGTAGTAAAATTCTATCTCCCGCGTTGGAAAGAAC-CGTTTGGAG-CCGGCCAGACAAC----------AAAAATT--TCTAT--GATT---- ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = Alignment_3) = N: 1-350; CODONPOSSET CodonPositions (CHARACTERS = Alignment_3) = N: 1-350; END; [ The following blocks are output data for analysis step 1060 ] BEGIN TREES; TITLE Tb5836; LINK TAXA = TaxaForAnalysisStep1060; TREE Fig._2 = [&R] (((Lecanora_garovaglii,Lecanora_varia),Ramalinora_glaucolivida,Lecanora_contractula,Lecanora_muralis,Lecanora_polytropa,Lecanora_glabrata),(Ramalina_fraxinea,((Ramalina_menziesii,Ramalina_leptocarpha),(Ramalina_intermedia,Ramalina_sinensis,Ramalina_montagnei)))Ramalina)Ramalinaceae; [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr5527] END;