#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 April 23, 2024; 17:06 GMT TreeBASE (cc) 1994-2008 Study reference: Dentinger B., & Mclaughlin D. 2006. Reconstructing the Clavariaceae using nuclear large subunit rDNA sequences and a new genus segregated from Clavaria. Mycologia, 98(5): 746-762. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S1699] [ The following blocks are input data for analysis step 3358 ] BEGIN TAXA; TITLE TaxaForAnalysisStep3358; DIMENSIONS NTAX=11; TAXLABELS Bulbillomyces_farinosus Henningsomyces_candidus Macrotyphula_defibulata Macrotyphula_fistulosa Macrotyphula_juncea_DJM_1032 Macrotyphula_juncea_DJM_975 Phyllotopsis_nidulans Pleurocybella_porrigens Typhula_phacorrhiza_AF393079 Typhula_phacorrhiza_AY586724 Typhula_phacorrhiza_DAOM195241 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M913] TITLE Macrotyphula_clade_28S_rDNA; LINK TAXA = TaxaForAnalysisStep3358; DIMENSIONS NCHAR=870; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=N 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 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Bulbillomyces_farinosus GAAGCGGGAAAAGCTCAAATTTAAAATCTGGCGGT{CT}CTTGTAGCCGTCCGAGTTGTAATTTAGAGAAGTGTTATCCGCGCTGGACCGTGTATAAGTCTCCTGGAACGGAGCGTCGTAGAGGGTGAGAATCCCGTATATGACACGGACTACCAGGGCTTTGTGATGCGCTCTCGAAGAGTCGAGTTGTTTGGGAATGCAGCTCAAAATGGGTGGTAAATTCCATCTAAAGCTAAATATAGGCGAGAGACCGATAGCGAACAAGTACCGTGAGGGAAAGATGAAAAGAACTTTGGAAAGAGAGTTAAACAGTACGTGAAATTGTTGAAAAGGAAACGCTTGAAGTCAGTCGCGTTAGCCAGGGATCAACTTAGC--TTTT-GCTGAGAGCACTTTCTGGTTGACGGGTCAGCATCAATTTTGATTGTTGGATAAAGGTCAGTGGAATGTGGCATCCTCGGATGTGTTATAGCCATTGGTTCGTATACAACAGTTGGGATTGAGGAACTCAGCACGCCGCAAGGCCGGG--TATTC--GTACCAC-GTA--CGTGCTTAGGATGCTGGCATAATGGCTTTAATCGACCCGTCTTGAAACACGGACCAAGGAGTCTAACATGCCCGCGAGTGTTTGGGTGTAAAACCCGAGCGCGTAATGAAAGTGAAAGTTCAGACCTCTGTCGTGGAGGGCATTGACGCCCGGACCAGACCTTTTGTGACGGATCCGCGGTAGAGCGTGTATGTTGGGACCCGAAAGATGGTGAACTATGCCTGAATAGGGTGAAGCCAGAGGAAACTCTGGTGGAGGCTCGTAGCGATTCTGACGTGCAAATCGATCGTCGAATTTGGGTATAGGGGCGAAAGACTAATCG Henningsomyces_candidus GAAGCGGGAAGAGCTCAAATTTAAAATCTGGCAGTCCTTGTGATTGTCCGAGTTGTAATTTAGAGAAGTGCTATCCGCGCTGGACCGTGTACAAGTCTGCTGGAACGCAGCGTCGTAGAGGGTGAGAATCCCGTAT{AT}TGACACGGACTACCAGGGCTTTGTGATGCGCTCTCGAAGAGTCGAGTTGTTTGGGAATGCAGCTCAAAATGGGTGGTAAATTCCATCTAAAGCTAAATATAGGCGAGAGACCGATAGCGAACAAGTACCGTGAGGGAAAGATGAAAAGAACTTTGGAAAGAGAGTTAAACAGTACGTGAAATTGTTGAAAGGGAAACGCTTGAAGTCAGTCGCGTCGTCTAGAAATCAACCTTGC--TTTT-GCTGGGAGCACTTTCTAGTTGACGGGTCAGCATCAGTTTTGATTGTTGGATAAAGGTTGGAGGAATGTGGCATCTCCGGATGTGTTATAGCCTCTGATTCACATACGACAGTTGGGACTGAGGAACTCAGCACGCCGCAAGGCCGGG--TTTTT--A-ACCAC-GTAA-CGTGCTTAGGATGCTGGCATAATGGCTTTAATCGACCCGTCTTGAAACACGGACCAAGGAGTCTAACATGCCTGCGAGTATTTGGGTGGAAAACTCGAATGCGTAATGAAAGTGATAGTTGAGATCTCTGTCGTGGAGAGCATCGACGCCCGGACCAGACCTTCTGTGACGGATCCGCGGTAGAGCATGTATGTTGGGACCCGAAAGATGGTGAACTATGCCTGAATAGGGTGAAGCCAGAGGAAACTCTGGTGGAGGCTCGTAGCGATTCTGACGTGCAAATCGATCGTCGAATTTGGGTATAGGGGCGAAAGACTAATCG Macrotyphula_defibulata GAAGCGGGAAAAGCTCAAATTTAAAATCTGATAGTCCTTGTGGCTGTCCGAGTTGTAATTTAGAGAAGTGTTATCCGCGCTGGACCGTGTATAAGTCTCCTGGAACGGAGCGTCGTAGAGGGTGAGAATCCCGTATATGACACGGACTACCAGGGCTTTGTGATGCGCTCTCAAAGAGTCGAGTTGTTTGGGATTGCAGCTCAAAATGGGTGGTAAATTCCATCTAAAGCTAAATATAGGCGAGAGACCGATAGCGAACAAGTACCGTGAGGGAAAGATGAAAAGAACTTTGGAAAGAGAGTTAAACAGTACGTGAAATTGTTGAAAAGGAAACGCTTGAAGTCAGTCGCGTTGGCCGGGGATCAACTTAGC--TTTT-GCTGAGAGTACTTTCCGGTTAACGGGTCAGCATCAATTTTGATTGTTGGATAAAGGTCAGTGGAATGTGGCATCTTCGGATGTGTTATAGCCATTGGTTCGTATACAACAGTTGGGATTGAGGAACTCAGCACGCCGCAAGGCCGGG--TATTT--ATACCAC-GTA--CGTGCTTAGGATGCTGGCATAATGGCTTTAATCGACCCGTCTTGAAACACGGACCAAGGAGTCTAACATGCCCGCGAGTGTTTGGGTGATAAACCCGAGCGCATAATGAAAGTGAAAGTTGAGACCTCTGTCGTGGAGGGCATCGACGCCCGGACCAGACCTTTTGTGACGGATCCGCGGTAGAGCGTGTATGTTGGGACCCGAAAGANGGTGAACTATGCCTGAATAGGGTGAAGCCAGAGGAAACTCTGGTGGAGGCTCGTAGCGATTCNGACGTGCAAATCGATCGTCGAATTTGGGTATAGGGGCGAAAGACTAATCG Macrotyphula_fistulosa GA-GCGGGAAAAGCTCAAATTTAAAATCTGGCGGTTCTTGTAGCCGTCCGAGTTGTAATTTAGAGAAGTGTTATCCGCGCTGGACCGTGTATAAGTCTCCTGGAACGGAGCGTCGTAGAGGGTGAGAATCCCGTATATGACACGGACTACCAGGGCTTTGTGATGCGCTCTCGAAGAGTCGAGTTGTTTGGGAATGCAGCTCAAAATGGGTGGTAAATTCCATCTAAAGCTAAATATAGGCGAGAGACCGATAGCGAACAAGTACCGTGAGGGAAAGATGAAAAGAACTTTGGAAAGAGAGTTAAACAGTACGTGAAATTGTTGAAAAGGAAACGCTTGAAGTCAGTCGCGTTAGCCAGGGATCAACTTAGC--TTTT-GCTGAGAGCACTTTCTGGTTGACGGGTCAGCATCAATTTTGATTGTTGGATAAAGGTCAGTGGAATGTGGCATCCTCGGATGTGTTATAGCCATTGGTTCGTATACAACAGTTGGGATTGAGGAACTCAGCACGCCGCAAGGCCGGG--TATTC--GTACCAC-GTA--CGTGCTTAGGATGCTGGCATAATGGCTTTAATCGACCCGTCTTGAAACACGGACCAAGGAGTCTAACATGCCCGCGAGTGTTTGGGTGTAAAACCCGAGCGCGTAATGAAAGTGAAAGTTGAGACCTCTGTCGTGGAGGGCATCGACGCCCGGACCAGACCTTTTGTGACGGATCCGCGGTAGAGCGTGTATGTTGGGACCCGAAAGATGGTGAACTATGCCTGAATAGGGTGAAGCCAGAGGAAACTCTGGTGGAGGCTCGTAGCGATTCTGACGTGCAAATCGATCGTCGAATTTGGGTATAGGGGCGAAAGACTAATCG Macrotyphula_juncea_DJM_1032 GAAGCGGGAAAAGCTCAAATTTAAAATCTGATAGTCCTTGCGGCTGTCCGAGTTGTAATTTAGAGAAGTGTTATCCGCGCTGGACCGTGTATAAGTCTCCTGGAACGGAGCGTCGTAGAGGGTGAGAATCCCGTATATGACACGGACTACCAGGGCTTTGTGATGCGCTCTCAAAGAGTCGAGTTGTTTGGGAATGCAGCTCAAAATGGGTGGTAAATTCCATCTAAAGCTAAATATAGGCGAGAGACCGATAGCGAACAAGTACCGTGAGGGAAAGATGAAAAGAACTTTGGAAAGAGAGTTAAACAGTACGTGAAATTGTTGAAAAGGAAACGCTTGAAGTCAGTCGCGTTGGCCGGGGATCAACTTAGC--TTTT-GCTGAGAGCACTTTCCGGTTAACGGGTCAGCATCAATTTTGATTGTTGGATAAAGGTCAGTGGAATGTGGCATCTTCGGATGTGTTATAGCCATTGGTTCGCATACAACAGTTGGGATTGAGGAACTCAGCACGCCGCAAGGCCGGG--TATTT--ATACCAC-GTA--CGTGCTTAGGATGCTGGCATAATGGCTTTAATCGACCGGTCTTGAAACACGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Macrotyphula_juncea_DJM_975 GAAGCGGGAAAAGCTCAAATTTAAAATCTGATAGTCC-----GCTGTCCGAGTTGTAATTTAGAGAAGTGTTATCCGCGCTGGACCGTGTATAAGTCTCCTGGAACGGAGCGTCGTAGAGGGTGAGAATCCCGTATATGACACGGACTACCAGGGCTTTGTGATGCGCTCTCAAAGAGTCGAGTTGTTTGGGAATGCAGCTCAAAATGGGTGGTAAATTCCATCTAAAGCTAAATATAGGCGAGAGACCGATAGCGAACAAGTACCGTGAGGGAAAGATGAAAAGAACTTTGGAAAGAGAGTTAAACAGTACGTGAAATTGTTGAAAAGGAAACGCTTGAAGTCAGTCGCGTTGGCCGGGGATCAACTTAG---TTTT-GCTGAGAGCACTTTCCGGTTAACGGGTCAGCATCAATTTTGATTGTTGGATAA-GGTCAGTGGAATGTGGCATCTTCGGATGTGTTATAGCCATTG-TTCGCATACAACAGTTGGGATTGAGGAACTCAGCAC------------------------------------CGTGCTTAGGATGCTGGCATAATGGCTTTAATCGACCGGTCTTGAAACACGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Phyllotopsis_nidulans GAAGCGGGAAAAGCTCAAATTTAAAATCTGGCGGTCTCT--GATCGTCCGAGTTGTAATTTAGAGAAGTGTTATCCGCGCTGGACCGTGTACAAGTCTCCTGGAACGGAGCGTCATAGAGGGTGAGAATCCCGTATATGGCACGGACTACCAGGGCTTTGTGATGCGCTCTCGAAGAGTCGAGTTGTTTGGGAATGCAGCTCAAAATGGGTGGTAAATTCCATCTAAAGCTAAATATAGGCGAGAAACCGATAGCGAACAAGTACCGTGAGGGAAAGATGAAAAGAACTTTGGAAAGAGAGTTAAACAGTACGTGAAATTGTTGAAAGGGAAACGCTTGAAGTCAGTCGCGTTGGCCAAGGATCAACCTAGC-TTTTTTGCTGGGAGCACTTCTTGGTTGACGGGTCAGCATCAGTTTTGATTGTTGGATAAAGTTCAAGGGAATGTGGCATCTTCGGATGTGTTATAGCCTTTG-TTCGTATACAACAGTTGGGACTGAGGAACTCAGCATGCCGCAAGGCCGAG--TACTTTTGTACTAANGTAAACATGCTTAGGATGCTGGCATAATGGCTTTAATCGACCCGTCTTGAAACACGGACCAAGGAGTATAACATGCCCGCGAGTGTTTGGGTGGAAAACCCGAGCGCGTAATGAAAGTGAAAGTTGAGATCTCTGTCGTGGAGAGCATCGACGCCCGGACCAGACCTTTTGTGACGGTTCCGCGGTAGAGCGTGTATGTTGGGACCCGAAAGATGGTGAACTATGCCTGAATAGGGTGAAGCCAGAGGAAACTCTGGTGGAGGCTCGTAGCGATTCTGACGTGCAAATCGATCGTCGAATTTGGGTATAGGGGCGAAAGACTAATCG Pleurocybella_porrigens GAAGCGGGAAAAGCTCAAATTTAAAATCTGGCAATCCTCGTGGTTGTCCGAGTTGTAATTTAGAGAAGTGCTATCTGCGTTGGACCGTGTACAAGTCTCCTGGAACGGAGCGTCGTAGAGGGTGAGAATCCCGTATATGACACGGACTACCAAGGCTTTGTGATACGCTCTCAAAGAGTCGAGTTGTTTGGGAATGCAGCTCAAAATGGGTGGTAAATTCCATCTAAAGCTAAATATAGGCGAGAGACCGATAGCGAACAAGTACCGTGAGGGAAAGATGAAAAGAACTTTGGAAAGAGAGTTAAACAGTACGTGAAATTGTTGAAAGGGAAACGCTTGAAGTCAGTCGCGTTGTCCAGGAATCAACCTTGCATTTTTTGCTGGGAGCACTTTCTGGTTGACGGGTCAGCATCAATTTTGATTGTTGGATAAAGGTTAAGGGAATGTGGCATCCTCGGATGTGTTATAGCCCTTGATTCGCATACAACAGTTGGGATTGAGGAACTCAGCACGCCGCAAGGCCGGG--TACTT--GTACCAC-GTAA-CGTGCTTAGGATGCTGGCATAATGGCTTTAATCGACCCGTCTTGAAACACGGACCAAGGAGTCTAACATGCCCGCGAGTGTTTGGGTGGAAAACCCGAGCGCGTAATGAAAGTGAAAGTTGAGACCTCTGTCATGGAGGGCATCGACGCCCGGACCAGACCTTTTGTGACGGTCCCGCGGTAGAGCGTGTATGTTGGGACCCGAAAGATGGTGAACTATGCCTGAATAGGGTGAAGCCAGAGGAAACTCTGGTGGAGGCTCGTAGCGATTCTGACGTGCAAATCGATCGTCGAATTTGGGTATAGGGGCGAAAGACTAATCG Typhula_phacorrhiza_AF393079 GAAGCGGGAAAAGCTCAAATTTAAAATCTGATGGTCCTTGCGGCTGTCCGAGTTGTAATTTAGAGAAGTGTTATCCGCGCTGGACCGTGTATAAGTCTCCTGGAACGGAGCGTCGTAGAGGGTGAGAATCCCGTATATGACACGGACTACCAGGGCTTTGTGATGCGCTCTCAAAGAGTCGAGTTGTTTGGGATTGCAGCTCAAAATGGGTGGTAAATTCCATCTAAAGCTAAATATAGGCGAGAGACCGATAGCGAACAAGTACCGTGAGGGAAAGATGAAAAGAACTTTGGAAAGAGAGTTAAACAGTACGTGAAATTGTTGAAAAGGAAACGCTTGAAGTCAGTCGCGTTGGCCAGGGATCAACTTAGC--TTCT-GCTGAGAGCACTTTCTGGTTAACGGGTCAGCATCAATTTTGATCGTTGGATAAAGGTCAGTGGAATGTGGCATCTTCGGATGTGTTATAGCCATTGGTTCGTATACAACGGTTGGGATTGAGGAACTCAGCACGCCGCAAGGCCGGG--TATTC--GTACCAC-GTA--CGTGCTTAGGATGCTGGCATAATGGCTTTAATCGACCCGTCTTGAAACACGGACCAAGGAGTCTAACATGCCCGCGAGTGTTTGGGTGATAAACCCGAGCGCGTAATGAAAGTGAAAGTTGAGACCTCTGTCGTGGAGGGCATCGACGCCCGGACCAGACCTTTTGTGACGGATCCGCGGTAGAGCGTGTATGTTGGGACCCGAAAGATGGTGAACTATGCCTGAATAGGGTGAAGCCAGAGGAAACTCTGGTGGAGGCTCGTAGCGATTCTGACGTGCAAATCGATCGTCGAATTTGGGTATAGGGGCGAAAGACTAATCG Typhula_phacorrhiza_AY586724 GAAGCGGGAAAAGCTCAAATTTAAAATCTGGCGGTCCTTGTGGCCGTCCGAGTTGTAATTTAGAGAAGTGTTATCCGCGTTGGACCGTGTACAAGTCTCCTGGAACGGAGCGTCGTAGAGGGTGAGAATCCCGTATATGACACGGACTACCAAGGCTTTGTGATGCGCTCTCGAAGAGTCGAGTTGTTTGGGAATGCAGCTCAAAATGGGTGGTAAATTCCATCTAAAGCTAAATACAGGCGAGAGACCGATAGCGAACAAGTACCGTGAGGGAAAGATGAAAAGAACTTTGGAAAGAGAGTTAAACAGTACGTGAAATTGTTGAAAAGGAAACGCTTGAAGTCAGTCGCGTTGGCCGGGGATCAACTTGGC-TTTTTAGCTGAGAGCACTTTCCGGTCGACGGGTCAACATCAATTTTGATTGTTGGATAAAGGTCAGTGGAATGTGGCATCTTCGGGTGTGTTATAGCCATTGGTTCGCATACAACGGTTGGGATTGAGGAACTCAGTACGCCGCAAGGCCGGA--TAGCA--ATATCAC-GTA--CGTACTTAGGATGTTGGCATAATGGCTTTAATCGACCCGTCTTGAAACACGGACCAAGGAGTCTAACATGCCCGCGAGTGTTTGGGTGGAAAACCCGAGCGCGTAATGAAAGTGAAAGTTGAGATCCCTGTCGTGGGGAGCATCGACGCCCGGACCAGACCTTTTGTGACGGATCCGCGGTAGAGCGTGTATGTTGGGACCCGAAAGATGGTGAACTATGCCTGAATAGGGTGAAGCCAGAGGAAACTCTGGTGGAGGCTCGTAGCGATTCTGACGTGCAAATCGATCGTCGAATTTGGGTATAGGGGCGAAAGACTAATCG Typhula_phacorrhiza_DAOM195241 GAAGCGGGAAAAGCTCAAATTTAAAATCTGGCGGTCCTTGTGGCCGTCCGAGTTGTAATTTAGAGAAGTGTTATCCGCGTTGGACCGTGTACAAGTCTCCTGGAACGGAGCGTCGTAGAGGGTGAGAATCCCGTATATGACACGGACTACCAAGGCTTTGTGATGCGCTCTCGAAGAGTCGAGTTGTTTGGGAATGCAGCTCAAAATGGGTGGTAAATTCCATCTAAAGCTAAATATAGGCGAGAGACCGATAGCGAACAAGTACCGTGAGGGAAAGATGAAAAGAACTTTGGAAAGAGAGTTAAACAGTACGTGAAATTGTTAAAAAGGAAACGCTTGAAGTCAGTCGCGTTAACCGGGGATCAACTTGGC-TTTCTAGCTGAGAGCACTTTCCGGTTGACGGGTCAACATCAATTTTGACTGTTGGATAAAGGTCAGTGGAATGTGGCATCTTCGGGTGTGTTATAGCCATTGGTTCGCATACAACGGTTGGGATTGAGGAACTCAGCACGCCGCAAGGCCGGA--GATTC--GTCTCAC-GTA--CGTGCTTAGGATGTTGGCATAATGGCTTTAATCGACCCGTCTTGAAACACGGACCAAGGAGTCTAACATGCCCGCGAGTGTTTGGGTGGAAAACCCGAGCGCGTAATGAAAGTGAAAGTTGAGATCCCTGTCGTGGGGAGCATCGACGCCCGGACCAGACCTTTTGTGACGGATCCGCGGTAGAGCGTGTATGTTGGGACCCGAAAGATGGTGAACTATGCCTGAATAGGGTGAAGCCAGAGGAAACTCTGGTGGAGGCTCGTAGCGATTCTGACGTGCAAATCGATCGTCGAATTTGGGTATAGGGGCGAAAGACTAATCG ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = Macrotyphula_clade_28S_rDNA) = N: 1-870; CODONPOSSET CodonPositions (CHARACTERS = Macrotyphula_clade_28S_rDNA) = N: 1-870; END; [ The following blocks are output data for analysis step 3358 ] BEGIN TREES; TITLE Tb8131; LINK TAXA = TaxaForAnalysisStep3358; TREE Macrotyphula_MP = [&R] (Macrotyphula_juncea_DJM_975,(Macrotyphula_juncea_DJM_1032,((Typhula_phacorrhiza_AF393079,(((Typhula_phacorrhiza_AY586724,Typhula_phacorrhiza_DAOM195241),((Henningsomyces_candidus,Pleurocybella_porrigens),Phyllotopsis_nidulans)),(Macrotyphula_fistulosa,Bulbillomyces_farinosus))),Macrotyphula_defibulata))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr4738] END;