#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 March 30, 2026; 19:22 GMT TreeBASE (cc) 1994-2008 Study reference: Tooley P., Goley E., Carras M., Frederick R., Weber E., & Kuldau G. 2000. Characterization of Claviceps species pathogenic on sorghum by sequence analysis of the beta-tubulin gene intron 3 region and EF-1 alpha gene intron 4. Mycologia, 93(3): 541-551. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S943] [ The following blocks are input data for analysis step 1593 ] BEGIN TAXA; TITLE TaxaForAnalysisStep1593; DIMENSIONS NTAX=12; TAXLABELS Claviceps_africana_cla2 Claviceps_africana_cla7 Claviceps_africana_cls1 Claviceps_africana_cls2 Claviceps_fusiformis_clf1 Claviceps_paspali_cpas1 Claviceps_paspali_cpas2 Claviceps_purpurea_clp1 Claviceps_purpurea_clp2 Claviceps_sorghicola_cjap2 Claviceps_sorghicola_cjap4 taxon_12 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M3560] TITLE ef1; LINK TAXA = TaxaForAnalysisStep1593; DIMENSIONS NCHAR=418; 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 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Claviceps_africana_cla2 CATCGAGAAGTTCGAGAAGGTAAGA-----GTTTTTCCTCGC-C---TCG-TGCC--------------GTTATCTTCT-----------------------TCCTTTCGGCTACAGTGG------CCTGCAAGCATGGTGGCT-ACCCCTC-ATTCCTCCGCGACACGAAG-AATTTTCTTCTCGGGTTGCGAGTGTC---------AGCCCGCG-TTGCC-TGGT-GTACCTTTC--AATCCGTCACTTGTTTTCGATGGAGCAATGGGCG--AGCGTGATG-AACGCAGCTTTC---CA-CGTG--TG-----AACGATGATGAGGA---GAAGT--AAA----CAGGA-A-AGTCGCTGACCACCTTTT-GATGTATAGGAAGCCGCCGAACTCGGTAAGGGTTCCTTCAAGTA Claviceps_africana_cla7 CATCGAGAAGTTCGAGAAGGTAAGA-----GTTTTTCCTCGC-C---TCG-TGCC--------------GTTATCTTCT-----------------------TCCTTTCGGCTACAGTGG------CCTGCAAGCATGGTGGCT-ACCCCTC-ATTCCTCCGCGACACGAAG-AATTTTCTTCTCGGGTTGCGAGTGTC---------AGCCCGTG-TTGCC-TGGT-GTACCTTTC--AATCCGTCACTTGTTTTCGATGGAGCAATGGGCG--AGCGTGATG-AACGCAGCTTTC---CA-CGTG--TG-----AACGATGATGAGGA---GAAGT--AAA----CAGGA-A-AGTCGCTGACCACCTTTT-GATGTATAGGAAGCCGCCGAACTCGGTAAGGGTTCCTTCAAGTA Claviceps_africana_cls1 CATCGAGAAGTTCGAGAAGGTAAGA-----GTTTTTCCTCGC-C---TCG-TGCC--------------GTTATCTTCT-----------------------TCCTTTCGGCTACAGTGG------CCTGCAAGCATGGTGGCT-ACCCCTC-ATTCCTCCGCGACACGAAG-AATTTTCTTCTCGGGTTGCGAGTGTC---------AGCCCGTG-TTGCC-TGGT-GTACCTTTC--AATCCGTCACTTGTTTTCGATGGAGCAATGGGCG--AGCGTGATG-AACGCAGCTTTC---CA-CGTG--TG-----AACGATGAT---GA---GAAGT--AAA----CAGGA-A-AGTCGCTGACCACCTTTT-GATGTATAGGAAGCCGCCGAACTCGGTAAGGGTTCCTTCAAGTA Claviceps_africana_cls2 CATCGAGAAGTTCGAGAAGGTAAGA-----GTTTTTCCTCGC-C---TCG-TGCC--------------GTTATCTTCT-----------------------TCCTTTCGGCTACAGTGG------CCTGCAAGCATGGTGGCT-ACCCCTC-ATTCCTCCGCGACACGAAG-AATTTTCTTCTCGGGTTGCGAGTGTC---------AGCCCGTG-TTGCC-TGGT-GTACCTTTC--AATCCGTCACTTGTTTTCGATGGAGCAATGGGCG--AGCGTGATG-AACGCAGCTTTC---CA-CGTG--TG-----AACGATGAT---GA---GAAGT--AAA----CAGGA-A-AGTCGCTGACCACCTTTT-GATGTATAGGAAGCCGCCGAACTCGGTAAGGGTTCCTTCAAGTA Claviceps_fusiformis_clf1 -GCTTTTTT-TTCTTGTTCACGTCGATTTCAGA-----------GATTGCTTGCGCG------GTCACCAAAGTGTGAATTTGATTCTACCTTAG------CGGGCATGCAATGTG-----CCCCTCTTTGAGGCAG-GACTCGAAAAAA----ATTCTTCAGCCGTGGGGCTCACCCTCTCATGTCTGA-CTCGCCGAGGCGGGGTGTCTCCACCTACCCCAATCCGTCCGGC--GAGCA-TGGA----ATTGCGCTGCGA--CATCTATCAATGAGCATGGCTGCGCAGAA-GATGA----------AAGTCCACACACATACGACATTGTCGCTGACCTGTTTT--AAACTATAGGAAGCCGCCGAACTCGGTAAGGGTTCCTTCAAGTAC-A{ACG}-C--{CG}--T{CG}---{AG}{AC}-{CG}-C--C Claviceps_paspali_cpas1 -G---TCGTTTTCACAAACCAGGCCGTGTCCGCTCGCCGTC-GTCCGCCA------TAAGTTGCTTCTGCTGCTGTGGATGTGACGGTCAAGCGTGGT-ACT-ACCACTC-TTTTGGCCGCGCCTCGA---AATTTT-TTCTTCGGTCGCGGGACTCCATTAGTTGGGTCTGACTTTGCC-TAGTGGGGCATCCC-GTCTCC-TCACTTAGCTGAGCTGGTGATGCAGACG-AAGGGTGCTCCTATCC--CTCCT---CA-AGTG--TGGATACAAC-ATCAGGAAGATAGGAACA--AATGAGGCAAGTCA-TGTTGCTGACCTGGTTTTCGAATTGTAGGAAGCCGCCGAACTCGGTAAGGGTTCCTTCAAGTAC-A{ACG}-C--{CG}--A{CG}-A---C-A{CG}CCATCGAGAAGTTCGAGAAG Claviceps_paspali_cpas2 -----TATTTC-CTCTC-C---TCCCTCCCCTTAA------------AAACCCTGC----CAAGCCAGTATTGTGTGTCTTTTTTGAGTCACTAGCT-----AGGCATGCCAG-T--TTTGCCCCTCTT----------------TTGTC-TTTTTTTTTC--TCTC------C---------ACTTGGATCTTTTC--AGTGGAGCATC-CTCAACCCCTCA----TCTCAGATGGAA-----GACGC-AACG-------CCTCGGATGAC--TCC-CCTG--TTCATCCAACAAGGA-------------C--AAATGACCTGGACA-TGTCGCTGACTAGAC-TC-GAATTATAGGAAGCTGCCGAACTTGGTAAGGGTTCCTTCAAGTAC-A{ACG}-C--{CG}--A{CG}-A---C-A{CG}GCA Claviceps_purpurea_clp1 -----TATATCTCTTTCAC---TCC--ACGCATAATATGTGACGTTCAGTCGTTGCAATGCGAGCCTGCCTTGCGTGTCGCTTTGCAACCTCAAGGT-----GGGCAAGCAAGCG--ACTGCCCCTCTTTTCGCCCGCGATACGATTTTTTTTTTTTTTTCGGTCGCGGGGCTC---------AGTTTGA-CTTTT---GGTGGGGCACCTCTCAACCCGTCACTGGTCTGTGCTAG-A-----GACGCAAACGAGAGATACAAC--ATGACATTCG-CGTG--ATCTCCCAAAAA-------------------AAATGTGAT-GACA-AATCACTGACTTGCCTTT-GCTCTACAGGAAGCCGCCGAACTCGGAAAGGGTTCCTTCAAGTAC-A{ACG}-C--{CG}--T{AG}-T{AG}-A-C--CCA Claviceps_purpurea_clp2 CATCGAGAAGTTCGAGAAGGTAAGA-----GCTTT--CTTCC-C---TCA-TGCCACACGTTTAGCTTTGTTCTCTCCTGCGA-GCATGCCA------TAAGCCATTTCGGCTA---TGG------CGAGCAAGCATGGTGCCTGGCCCCTCTTTTTGACCGCGACTCGAAGAAATTTTTTTCTCCGGTTGC--GGGTC---------AGTCCGAC-TTTTT-TGGTGGGGCGTTTC-AAACCCCTCACTTGTCCTAGCTGGAAGAGCGGACG--ATCGTGATGCCACTCAGCTT-----CA-CGTG--TG-----ACCG-TGAACAACAT--GAACG--AAT----CAATACA-GGTTGCTGATCACCTTTC-GAATTACAGGAAGCCGCCGAACTCGGTAAGGGTTCCTTCAAGTA Claviceps_sorghicola_cjap2 -----TATTTC-CTCTC-C---TCCCTCCCCTTAA------------AAACCCTGC----CAAGCCAGTATTGTGTGTCTTTTTTGAGTCACTAGCT-----AGGCATGCCAG-T--TTTGCCCCTCTT----------------TTGTCTTTTTTTTTTC--TCTC------C---------ACTTGGATCTTTTC--AGTGGAGCATC-CTCAACCCCTCA----TCTCAGATGGAA-----GACGC-AACG-------CCTCGGATGAC--TCC-CCTG--TTCATCCAACAAGGA-------------C--AAATGACCTGGACA-TGTCGCTGACTAGAC-TC-GAATTATAGGAAGCTGCCGAACTTGGTAAGGGTTCCTTCAAGTAC-A{ACG}-C--{CG}-{CG}-{AG}G{ACT}-C--A-C-A- Claviceps_sorghicola_cjap4 CATCGAGAAGTTCGAGAAGGTAAGA-----GCTTT--CTTCC-C---TCA-TGCCACACGTTTAGCTTTGTTCTCTCCTGCGA-GCATGCCA------TAAGCCATTTCGGCTA---TGG------CGAGCAAGCATGGTGCCTGGCCCCTCTTTTTGACCGCGACTCGAAGAAATTTTTTTCTCCGGTTGC--GGGTC---------AGTCCGAC-TTTTT-TGGTGGGGCGTTTC-AAACCCCTCACTTGTCCTAGCTGGAAGAGCGGACG--ATCGTGATGCCACTCAGCTT-----CA-CGTG--TG-----ACCG-TGAACAACAT--GAACG--AAT----CAATACA-GGTTGCTGATCACCTTTC-GAATTACAGGAAGCCGCCGAACTCGGTAAGGGTTCCTTCAAGTA taxon_12 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = ef1) = N: 1-418; CODONPOSSET CodonPositions (CHARACTERS = ef1) = N: 1-418; END; [ The following blocks are output data for analysis step 1593 ] BEGIN TREES; TITLE Tb6369; LINK TAXA = TaxaForAnalysisStep1593; TREE Fig._4 = [&R] (Claviceps_purpurea_clp1,(Claviceps_purpurea_clp2,(Claviceps_fusiformis_clf1,(((Claviceps_paspali_cpas1,Claviceps_paspali_cpas2),Epichloe_typhinia_200736),((Claviceps_sorghicola_cjap2,Claviceps_sorghicola_cjap4),((Claviceps_africana_cla2,Claviceps_africana_cla7,Claviceps_africana_cls2),Claviceps_africana_cls1)Claviceps_africana)))))Claviceps; [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr3650] END; BEGIN TREES; TITLE Tb6369; LINK TAXA = TaxaForAnalysisStep1593; TREE ef_PAUP_5 = [&R] (Claviceps_purpurea_clp1,(Claviceps_purpurea_clp2,(Claviceps_fusiformis_clf1,(((Claviceps_paspali_cpas1,Claviceps_paspali_cpas2),Epichloe_typhinia_200736),((Claviceps_sorghicola_cjap2,Claviceps_sorghicola_cjap4),((Claviceps_africana_cla2,Claviceps_africana_cla7,Claviceps_africana_cls1),Claviceps_africana_cls2)))))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr3646] END; BEGIN TREES; TITLE Tb6369; LINK TAXA = TaxaForAnalysisStep1593; TREE ef_PAUP_2 = [&R] (Claviceps_purpurea_clp1,(Claviceps_purpurea_clp2,(Claviceps_fusiformis_clf1,(((Claviceps_paspali_cpas1,Claviceps_paspali_cpas2),Epichloe_typhinia_200736),((Claviceps_sorghicola_cjap2,Claviceps_sorghicola_cjap4),((Claviceps_africana_cla2,Claviceps_africana_cla7),Claviceps_africana_cls1,Claviceps_africana_cls2)))))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr3645] END; BEGIN TREES; TITLE Tb6369; LINK TAXA = TaxaForAnalysisStep1593; TREE ef_PAUP_3 = [&R] (Claviceps_purpurea_clp1,(Claviceps_purpurea_clp2,(Claviceps_fusiformis_clf1,(((Claviceps_paspali_cpas1,Claviceps_paspali_cpas2),Epichloe_typhinia_200736),((Claviceps_sorghicola_cjap2,Claviceps_sorghicola_cjap4),(((Claviceps_africana_cla2,Claviceps_africana_cla7),Claviceps_africana_cls2),Claviceps_africana_cls1)))))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr3649] END; BEGIN TREES; TITLE Tb6369; LINK TAXA = TaxaForAnalysisStep1593; TREE ef_PAUP_7 = [&R] (Claviceps_purpurea_clp1,(Claviceps_purpurea_clp2,(Claviceps_fusiformis_clf1,(((Claviceps_paspali_cpas1,Claviceps_paspali_cpas2),Epichloe_typhinia_200736),((Claviceps_sorghicola_cjap2,Claviceps_sorghicola_cjap4),(Claviceps_africana_cla2,Claviceps_africana_cla7,Claviceps_africana_cls1,Claviceps_africana_cls2)))))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr3644] END; BEGIN TREES; TITLE Tb6369; LINK TAXA = TaxaForAnalysisStep1593; TREE ef_PAUP_1 = [&R] (Claviceps_purpurea_clp1,(Claviceps_purpurea_clp2,(Claviceps_fusiformis_clf1,(((Claviceps_paspali_cpas1,Claviceps_paspali_cpas2),Epichloe_typhinia_200736),((Claviceps_sorghicola_cjap2,Claviceps_sorghicola_cjap4),(((Claviceps_africana_cla2,Claviceps_africana_cla7),Claviceps_africana_cls1),Claviceps_africana_cls2)))))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr3648] END; BEGIN TREES; TITLE Tb6369; LINK TAXA = TaxaForAnalysisStep1593; TREE ef_PAUP_6 = [&R] (Claviceps_purpurea_clp1,(Claviceps_purpurea_clp2,(Claviceps_fusiformis_clf1,(((Claviceps_paspali_cpas1,Claviceps_paspali_cpas2),Epichloe_typhinia_200736),((Claviceps_sorghicola_cjap2,Claviceps_sorghicola_cjap4),(Claviceps_africana_cla2,(Claviceps_africana_cla7,Claviceps_africana_cls1,Claviceps_africana_cls2))))))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr3647] END;