#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 10, 2024; 13:58 GMT

TreeBASE (cc) 1994-2008

Study reference:
Chen S.F., Morgan D., Hasey J., Anderson K., & Michailides T.J. 2013. Phylogeny,
morphology, distribution, and pathogenicity of Botryosphaeriaceae and Diaporthaceae
from English walnut in California. Plant Disease, .

TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S14888]

[ The following blocks are input data for analysis step 12653 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep12653;
        DIMENSIONS NTAX=14;
        TAXLABELS
            Celoporthe_eucalypti_CMW26908
            Diaporthe_hickoriae_CBS145_26
            Diaporthe_neotheicola_58
            Diaporthe_neotheicola_CBS_123208
            Diaporthe_neotheicola_CBS_123209
            Diaporthe_rhusicola_45
            Diaporthe_rhusicola_46
            Diaporthe_rhusicola_59
            Diaporthe_rhusicola_63
            Diaporthe_rhusicola_64
            Diaporthe_rhusicola_73
            Diplodia_alleghaniensis_CBS_495_72
            Diplodia_rhusicola_CPC_18191_CBS_129528
            Phomopsis_vitivola_CBS114016
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M19799]

	TITLE File_4_Diaporthe_ITS;
	LINK TAXA = TaxaForAnalysisStep12653;
	DIMENSIONS NCHAR=627;
	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       ]
[                                                    .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .       ]
Celoporthe_eucalypti_CMW26908               ????????????????????????????????CCCAGATACCCCTATGTGAACTTATACCTTTTTAAAATCGTTGCCTCGGCGCCGAGCCCGGGGGAGACGGGATATAGAAATATCTTTTCTTTTCCCGCTCCCCTCCCTTCACCACCGTGCAAACGGTGTGTTGGTGGGAGCAGGCCCGCCGGCGGCCCGTTAAACTCTTGTTTTTAAA---AAACGTATCTCTTCTGAGTAATTAAACAAAAAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCTGGAATTCCAGCGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCTTGGCTTGGTGTTGGGGTACTACCCGTAA----AACGGTAGGCCCTGAAATTTAGTGGCGGGCTCGCTAAGACTCTGAGCGTAGTAGTGTTTTTTCTCAACCTCGCTTTGGAAGG-ATTAGCGGTTGCTCTTGCCGTAAAACCCCCCTATATTATTTTGAAAATTTGACCTCGGATCAGGTAGGAATACCCGCTGAACTTAA
Diaporthe_hickoriae_CBS145_26               AGGGATCATTGCTGGAACGCGCCCCAGGCGCACCCAGAAACCCTT-TGTGAACTTATACCTT------ACTGTTGCCTCGGCGCAGG----------------------------CCGGCCCCCGCGGGGGC----CCCTC----------------CTGTCCCAGGAGGAGCAGGCCCGCCGGCGGCCAAGCCAACTC-TGTTTTTACACTGGAAC--------TCTGAGT-ACAAAAC---ACAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATTCCGGAGGGCATGCCTGTCCGAGCGTCATTTCAACCCTCAAGCCTGGCTTGGTGTTGGGGCACTGCTCCCCCCCCGGGGAGCAGGCCCTGAAATACAGTGGCGGGCTCGCCAGGACTCCGAGCGCAGTAG-------TTAAACCCTCGCTCTGGAAGG-CCTGGCGGT--GCCCTGCCGTTAAACCCC-----AAC-TTCTGAAAATTTGACCTCGGATCAGGTAGGAATACCCGCTGAACTTAA
Diaporthe_neotheicola_58                    AGGGATCATTGCTGGAACGCGCCCCTGGCGCACCCAGAAACCCTT-TGTGAACTTATACCTT------ACTGTTGCCTCGGCGCAGG----------------------------CCGTCCCCTGATGGGGT----CCCTC----------------TGGAGAC-AGAGGAGCA-GCCGGCCGGTGGCCAAATTAACTC-TGTTTTTACACTGAAAC--------TCTGAGT-ACAAAAC---ATAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATTCCGGAGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCCTGGCTTGGTGTTGGGGCACTGCTCTCTGAC--GAGAGCAGGC??TGAAATATAGTGGCGAGCTCGCCAGGACTCCGAGCGTAGTAG-------TTAAACCCTCGCTTTGGAAGG-CCTGGCGGT--GCCCTGCCGTTAAACCCC-----AAC-TTCTGAAAATTTGACCTCGGATCAGGTAGGAATACCCGCTGAACTTAA
Diaporthe_neotheicola_CBS_123208            AGGGATCATTGCTGGAACGCGCCCCTGGCGCACCCAGAAACCCTT-TGTGAACTTATACCTT------ACTGTTGCCTCGGCGCAGG----------------------------CCGTCCCCTGATGGGGT----CCCTC----------------TGGAGAC-AGAGGAGCA-GCCGGCCGGTGGCCAAATTAACTC-TGTTTTTACACTGAAAC--------TCTGAGT-ACAAAAC---ATAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATTCCGGAGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCCTGGCTTGGTGTTGGGGCACTGCTCTCTGAC--GAGAGCAGGCCCTGAAATATAGTGGCGAGCTCGCCAGGACTCCGAGCGTAGTAG-------TTAAACCCTCGCTTTGGAAGG-CCTGGCGGT--GCCCTGCCGTTAAACCCC-----AAC-TTCTGAAAATTTGACCTCGGATCAGGTAGGAATACCCGCTGAACTTAA
Diaporthe_neotheicola_CBS_123209            AGGGATCATTGCTGGAACGCGCCCCTGGCGCACCCAGAAACCCTT-TGTGAACTTATACCTT------ACTGTTGCCTCGGCGCAGG----------------------------CCGTCCCCTGATGGGGT----CCCTC----------------TGGAGAC-AGAGGAGCA-GCCGGCCGGTGGCCAAATTAACTC-TGTTTTTACACTGAAAC--------TCTGAGT-ACAAAAC---ATAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATTCCGGAGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCCTGGCTTGGTGTTGGGGCACTGCTCTCTGAC--GAGAGCAGGCCCTGAAATATAGTGGCGAGCTCGCCAGGACTCCGAGCGTAGTAG-------TTAAACCCTCGCTTTGGAAGG-CCTGGCGGT--GCCCTGCCGTTAAACCCC-----AAC-TTCTGAAAATTTGACCTCGGATCAGGTAGGAATACCCGCTGAACTTAA
Diaporthe_rhusicola_45                      AGGGATCATTGCTGGAACGCGCCCCTGGCGCACCCAGAAACCCTT-TGTGAACTTATACCTT------ACTGTTGCCTCGGCGCAGG----------------------------CCGTCCCCTAACGGGGT----CCCTT----------------TTGTCTCAAAAGGAGCA-GCCGGCCGGTGGCCAAATTAACTC-TGTTTTTAAACTGAAAC--------TCTGAGT-AAAAAAC---ATAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATTCCGGAGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCCTGGCTTGGTGTTGGGGCACTGCTTTCTAAC--GAGAGCAGGCCCTGAAATATAGTGGCGAGCTCGCCAGGACTCCGAGCGTAGTAG-------TTAAACCCTCGCTTTGGAAGG-CCTGGCGGT--GCCCTGCCGTTAAACCCC-----AAC-TTCTGAAAATTTGACCTCGGATCAGGTAGGAATACCCGCTGAACTTAA
Diaporthe_rhusicola_46                      AGGGATCATTGCTGGAACGCGCCCCTGGCGCACCCAGAAACCCTT-TGTGAACTTATACCTT------ACTGTTGCCTCGGCGCAGG----------------------------CCGTCCCCTAACGGGGT----CCCTT----------------TTGTCTCAAAAGGAGCA-GCCGGCCGGTGGCCAAATTAACTC-TGTTTTTAAACTGAAAC--------TCTGAGT-AAAAAAC---ATAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATTCCGGAGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCCTGGCTTGGTGTTGGGGCACTGCTTTCTAAC--GAGAGCAGGCCCTGAAATATAGTGGCGAGCTCGCCAGGACTCCGAGCGTAGTAG-------TTAAACCCTCGCTTTGGAAGG-CCTGGCGGT--GCCCTGCCGTTAAACCCC-----AAC-TTCTGAAAATTTGACCTCGGATCAGGTAGGAATACCCGCTGAACTTAA
Diaporthe_rhusicola_59                      AGGGATCATTGCTGGAACGCGCCCCTGGCGCACCCAGAAACCCTT-TGTGAACTTATACCTT------ACTGTTGCCTCGGCGCAGG----------------------------CCGTCCCCTAACGGGGT----CCCTT----------------TTGTCTCAAAAGGAGCA-GCCGGCCGGTGGCCAAATTAACTC-TGTTTTTAAACTGAAAC--------TCTGAGT-AAAAAAC---ATAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATTCCGGAGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCCTGGCTTGGTGTTGGGGCACTGCTTTCTAAC--GAGAGCAGGCCCTGAAATATAGTGGCGAGCTCGCCAGGACTCCGAGCGTAGTAG-------TTAAACCCTCGCTTTGGAAGG-CCTGGCGGT--GCCCTGCCGTTAAACCCC-----AAC-TTCTGAAAATTTGACCTCGGATCAGGTAGGAATACCCGCTGAACTTAA
Diaporthe_rhusicola_63                      AGGGATCATTGCTGGAACGCGCCCCTGGCGCACCCAGAAACCCTT-TGTGAACTTATACCTT------ACTGTTGCCTCGGCGCAGG----------------------------CCGTCCCCTAACGGGGT----CCCTT----------------TTGTCTCAAAAGGAGCA-GCCGGCCGGTGGCCAAATTAACTC-TGTTTTTAAACTGAAAC--------TCTGAGT-AAAAAAC---ATAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATTCCGGAGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCCTGGCTTGGTGTTGGGGCACTGCTTTCTAAC--GAGAGCAGGCCCTGAAATATAGTGGCGAGCTCGCCAGGACTCCGAGCGTAGTAG-------TTAAACCCTCGCTTTGGAAGG-CCTGGCGGT--GCCCTGCCGTTAAACCCC-----AAC-TTCTGAAAATTTGACCTCGGATCAGGTAGGAATACCCGCTGAACTTAA
Diaporthe_rhusicola_64                      AGGGATCATTGCTGGAACGCGCCCCTGGCGCACCCAGAAACCCTT-TGTGAACTTATACCTT------ACTGTTGCCTCGGCGCAGG----------------------------CCGTCCCCTAACGGGGT----CCCTT----------------TTGTCTCAAAAGGAGCA-GCCGGCCGGTGGCCAAATTAACTC-TGTTTTTAAACTGAAAC--------TCTGAGT-AAAAAAC---ATAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATTCCGGAGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCCTGGCTTGGTGTTGGGGCACTGCTTTCTAAC--GAGAGCAGGCCCTGAAATATAGTGGCGAGCTCGCCAGGACTCCGAGCGTAGTAG-------TTAAACCCTCGCTTTGGAAGG-CCTGGCGGT--GCCCTGCCGTTAAACCCC-----AAC-TTCTGAAAATTTGACCTCGGATCAGGTAGGAATACCCGCTGAACTTAA
Diaporthe_rhusicola_73                      AGGGATCATTGCTGGAACGCGCCCCTGGCGCACCCAGAAACCCTT-TGTGAACTTATACCTT------ACTGTTGCCTCGGCGCAGG----------------------------CCGTCCCCTAACGGGGT----CCCTT----------------TTGTCTCAAAAGGAGCA-GCCGGCCGGTGGCCAAATTAACTC-TGTTTTTAAACTGAAAC--------TCTGAGT-AAAAAAC---ATAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATTCCGGAGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCCTGGCTTGGTGTTGGGGCACTGCTTTCTAAC--GAGAGCAGGCCCTGAAATATAGTGGCGAGCTCGCCAGGACTCCGAGCGTAGTAG-------TTAAACCCTCGCTTTGGAAGG-CCTGGCGGT--GCCCTGCCGTTAAACCCC-----AAC-TTCTGAAAATTTGACCTCGGATCAGGTAGGAATACCCGCTGAACTTAA
Diplodia_alleghaniensis_CBS_495_72          AGGGATCATTGCTGGAACGCGCCCCAGGCGCACCCAGAAACCCTT-TGTGAACTTATACCTT------ACTGTTGCCTCGGCGCTAG----------------------------CTGGCCCTCCGGGGCCCCTCACCCTC----------------GGGTGTTGAGACG-----GCCCGCCGGCGGCCAACCTAACTCTTGTTTTTACACTGAATC--------TCTGAGA-ATAAAAC---ATAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATTCCGGAGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCCTGGCTTGGTGATGGGGCACTGCTTTTACCC--AAAAGCAGGCCCTGAAATTCAGTGGCGAGCTCGCCAGGACCCCGAGCGCAGTAG-------TTAAACCCTCGCTTTGGAAGGCCCTGGCGGT--GCCCTGCCGTTAAACCCCC----AAC-TTCTGAAAATTTGACCTCGGATCAGGTAGGAATACCCGCTGAACTTAA
Diplodia_rhusicola_CPC_18191_CBS_129528     AGGGATCATTGCTGGAACGCGCCCCTGGCGCACCCAGAAACCCTT-TGTGAACTTATACCTT------ACTGTTGCCTCGGCGCAGG----------------------------CCGTCCCCTGATGGGGT----CCCTT----------------GGAAA---CGAGGAGCA-GCCGGCCGGTGGCCAAATTAACTC-TGTTTTTAAACTGAAAC--------TCTGAGT-ACAAAAC---ATAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATTCCGGAGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCCTGGCTTGGTGTTGGGGCACTGCTTTCTAAC--GAGAGCAGGCCCTGAAATATAGTGGCGAGCTCGCCAGGACTCCGAGCGTAGTAG-------TTAAACCCTCGCTTTGGAAGG-CCTGGCGGT--GCCCTGCCGTTAAACCCC-----AAC-TTCTGAAAATTTGACCTCGGATCAGGTAGGAATACCCGCTGAACTTAA
Phomopsis_vitivola_CBS114016                ??????????????????????????????????????AACCCTT-TGTGAACTCATACCTT------ACCGTTGCCTCGGCGCAGG----------------------------CCGGCCCCCCCTGGGGGGC--CCCTC----------------GGAGA---CGAGGAGCAGGCCCGCCGGCGGCCAAGTTAACTCTTGTTTTTACACTGAAAC--------TCTGAGAAACAAAAC---ACAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGTATTCCGGAGGGCATGCCTGTTCGAGCGTCATTTCAACCCTCAAGCCTGGCTTGGTGATGGGGCACTGCTCCCCCCCCGGGGAGCAGGCCCTGAAATCCAGTGGCGAGCTCGCCAGGACCCCGAGCGCAGTAG-------TTAAACCCTCGCTCCGGGAGGCCCTGGCGGT--GCCCTGCCGTTAAACCCCC----AAC-TTCTGAAAGTT?????????????????????????????????????
;
END;

[ The following blocks are output data for analysis step 12653 ]
BEGIN TREES;
      TITLE File_4_Diaporthe_ITS;
      LINK TAXA = TaxaForAnalysisStep12653;
      TREE PAUP_1 = [&R] (Celoporthe_eucalypti_CMW26908:0.26107911,(Diplodia_alleghaniensis_CBS_495_72:6.25E-5,((Diaporthe_hickoriae_CBS145_26:0.02517505,Phomopsis_vitivola_CBS114016:0.04743379):0.00813656,((Diaporthe_neotheicola_CBS_123208:1.0E-8,(Diaporthe_neotheicola_CBS_123209:1.0E-8,Diaporthe_neotheicola_58:1.0E-8):1.0E-8):3.42E-7,(Diplodia_rhusicola_CPC_18191_CBS_129528:0.00761596,(Diaporthe_rhusicola_45:1.0E-8,(Diaporthe_rhusicola_73:1.0E-8,((Diaporthe_rhusicola_46:1.0E-8,Diaporthe_rhusicola_59:1.0E-8):1.0E-8,(Diaporthe_rhusicola_63:1.0E-8,Diaporthe_rhusicola_64:1.0E-8):1.0E-8):1.0E-8):1.0E-8):0.01729232):0.01075193):0.05197377):0.08455184):0.26107911);
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr68974]


END;