#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 21, 2024; 22:15 GMT

TreeBASE (cc) 1994-2008

Study reference:
Guo L., Hyde K.D., & Liew E. 2001. Detection and taxonomic placement of endophytic
fungi within frond tissues of Livistona chinensis based on rDNA sequences. Molecular
Phylogenetics and Evolution, 20(1): 1-13.

TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S683]

BEGIN TAXA;
        TITLE  'P2-6b';
        DIMENSIONS NTAX=21;
        TAXLABELS
            Colletotrichum_acutatum
            Colletotrichum_capsici
            Colletotrichum_coccodes
            Colletotrichum_dematium
            Colletotrichum_destructivum
            Colletotrichum_fragariae
            Colletotrichum_fuscum
            Colletotrichum_kahawae
            Colletotrichum_lindemuthianum
            Colletotrichum_linicola
            Colletotrichum_musae
            Colletotrichum_orbiculare
            Colletotrichum_sublineolum
            Colletotrichum_trichellum
            Colletotrichum_trifolii
            Elsinoë_australis
            Glomerella_cingulata
            Glomerella_graminicola
            Hypocrea_rufa
            'P2-6'
            Saccharomyces_cerevisiae
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2264]

	TITLE 'ITS1 with P2-6';
	LINK TAXA = 'P2-6b';
	DIMENSIONS NCHAR=211;
	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 ]
[                                          .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         . ]
Colletotrichum_acutatum           CTGAGTT-ACCGCTCTATAACCCTTTGTGAAC-GTACCT--AACCGTTGCTTCGGCGGGC-AGGGGA---AGCCTCTCGCGGGCCT------CCCCTCCCGGCGCCGGCCCCCACCAC-----GGGGACGGGGCGCCCGCCGGAGG-AAA--CCAAA----CTCT-ATTT---ACACGACGTCTCTTCTGAGTGGCACAAGCAAATAATTA
Colletotrichum_capsici            CTGAGTT-ACCGCTCATCAACCCTTTGTGAAC-ATACCT-TAACTGTTGCTTCGGCGGGT-AGGCG-----TCCCCTAAAAAGGA-------CGTCTCCCGGCCCTCTCCCGTCC--------GCGGGTGGGGCGCCCGCCGGAGG-ATAA-CCAAA----CTCT-GATT---TAACGACGTTTCTTCTGAGTGACACAAGCAAATAATCA
Colletotrichum_coccodes           CTGAGTT-ACCGCTCTATAACCCTTTGTGAAC-ATACCT--AACTGTTGCTTCGGCGGGC-AGGGGGT---GCCGCC--TGCGGAC-----CCCCCTCCCGGCCCTGCCCTC--AC---------GGGCGGAGCGCCCGCCGGAGG-ATA--CCAAA----CTCT-ATTT---TAACGACGTTTCTTCTGAGTGGCACAAGCAAATAATTA
Colletotrichum_dematium           CTGAGTT-ACCGCTCTACAACCCTTTGTGAAC-ATACCT-TA-CTGTTGCTTCGGCGGGC-AG-------AGTCCCC-TCGGGGA-------CCCCTCCCGGCCCGTCCCTC--GC---------GGACGGAGCGCCCGCCGGAGG-ATA--CCAAA----CTCT-ATTT---TAACGACGTTTCTTCTGAGTGGCACAAGCAAATAATTA
Colletotrichum_destructivum       CTGAGTT-ACCGCTCTACAACCCTTTGTGAAC-ATACCT-TAACTGTTGCTTCGGCGGGC-AGGAGGACAACCCCCC-TCGGGGGG-CGGTCCCCCTCCCGGCCGCGCCCTC--AC---------GGGCGTGGCGCCCGCCGGAGG-ATA--CCAAAA---CTCT-ATTT---TAACGACGTTTCTTCTGAGTGGCACAAGCAAATAATTA
Colletotrichum_fragariae          CTGAGTT-TACGCTCTACAACCCTTTGTGAAC-ATACCTACAACTGTTGCTTCGGCGGGT-AGG-G-----TCCCCGT-----GA-------CC-CTCCCGGCCTCCCGCCCCCCC------GGCGGGTCGG-CGCCCGCCGGAGG-ATAA-CCAAA----CTCT-GATT---TAACGACGTTTCTTCTGAGTGGTACAAGCAAATAATCA
Colletotrichum_fuscum             CTGAGTT-TACGCTCTACAACCCTTTGTGAAC-ATACCTATAACTGTTGCTTCGGCGGGT-AGG-G-----TCTCCGC-----GA-------CC-CTCCCGGCCTCCCGCCTCCG-------CG-GGGTCGG-CGCCCGCCGGAGG-ATAA-CCAAA----CTCT-GATT---TAACGACGTTTCTTCTGAGTGGTACAAGCAAATAATCA
Colletotrichum_kahawae            CTGAGTT-TACGCTCTACAACCCTTTGTGAAC-ATACCTATAACTGTTGCTTCGGCGGGC-AGG-G-----TCTCCGT-----GA-------CC-CTCCCGGCCTCCCGCCCCCG-------GGCGGGTCGG-CGCCCGCCGGAGG-ATAA-CCAAA----CTCT-GATT---TAACGACGTTTCTTCTGAGTGGTACAAGCAAATAATCA
Colletotrichum_lindemuthianum     CTGAGTTTA-CGCTCTATAACCCTTTGTGAAC-ATACCA--AACCGTTGCTTCGGCGGGC-GGGAGG----TCCGCC-T-------------CCCC-CC-GGCCCCGCTCGC-----------------GGGGCGCCCGCCGGAGG-AAAA-CCCAA----CTCT-ATTT---TAACGACGTCTCTTCTGAGTGGCACAAGCAAATAGTCA
Colletotrichum_linicola           CTGAGTT-ACCGCTCTACAACCCTTTGTGAAC-ATACCT-TAACTGTTGCTTCGGCGGGC-AGGAGGACAACCCCCCCTCGGGGGGGCGGTCCCCCTCCCGGCCGCGCCCTC--AC---------GGGCGTGGCGCCCGCCGGAGG-ATA--CCAAA----CTCT-ATTT---TAACGACGTTTCTTCTGAGTGGCACAAGCAAATAATTA
Colletotrichum_musae              CTGAGTT-TACGCTCTGCAACCCTTTGTGAAC-ATACCTATAACTGTTGCTTCGGCGGGT-AGG-G-----TCCCCGT-----GA-------CC-CTCCCGGCCCCCCGCCCCCG-------GG-GCGTCGG-CGCCCGCCGGAGG-ATAA-CCAAA----CTCT-GATT---TAACGACGTTTCTTCTGAGTGGTACAAGCAAATAATCA
Colletotrichum_orbiculare         CTGAGTTTAACGCTCTATAACCCTTTGTGAAC-ATACCT--AACCGTTGCTTCGGCGGGC-GGGAGG----TCCGCC-T-------------CCCC-CCCGGCCCCGCTCGC-----------------GGGGAGCCCGCCGGAGG-AAAAACCCAA----CTCTTATTT---TAACGACGTCTCTTCTGAGTGGCACAAGCAAATAATCA
Colletotrichum_sublineolum        CTGAGTT-ACCGCTCTATAACCCTTTGTGAAC-ATACCT--AACTGTTGCTTCGGCGGGTTAGGGGG----TCCCTC--CGGGGA------CGCCCTCCCGCCGGCGCCCTCCTCCTCCGGGAGGGGTCGCGGCGCCCGCCGGAGG-ATAA-CCAAA----CTCT-GATT---TAACGACGTTTCTTCTGAGTGGCACAAGCAAATAATTA
Colletotrichum_trichellum         CTGAGTT-ACCGCTCTACAACCCTTTGTGAAC-ATACCT--AACTGTTGCTTCGGCGGGC-AGGAGG----TCCCCC--CGGGGA------CCCCCTCCCGGCCCCGCCCTC--GC---------AGGCGGAGCGCCCGCCGGAGG-TCA--CCAAACTC-TTAT-TTTT---TAGCGACGTTTCTTCTGAGTGGCACAAGCAAATAATAA
Colletotrichum_trifolii           CTGAGTTTA-CGCTCCATAACCCTTTGTGAAC-ATACCT--AACCGTTGCTTCGGCGGGC-GGGAGG----TCCGCC-T-------------CCCC-CCCGGCCCCGCTCGC-----------------GGGGCGCCCGCCGGAGG-AAAACCCCAA----CTCTTATTT---TAACGACGTCTCTTCTGAGTGGCACAAGCAAATAATCA
Elsinoë_australis                 CCGAAAGGA-GCCCGAACTCCCCACCCTTTGCTGTTGCG-AATCTGTTGCTTCGGCGGGCCCGC-------CCCCCCATCCCTGGG----GGGGCGGCCGGGCCTCACCGCCC-------------GGACAG-CGCCCGCCGGAGG----A-CCGAATCAACTCTGTTTTTAACCATAATGTCGGAGTACTTTTGTACAATCAAATTAAAA
Glomerella_cingulata              CTGAGTT-TACGCTCTATAACCCTTTGTGAAC-ATACCTATAACTGTTGCTTCGGCGGGT-AGG-G-----TCTCCGC-----GA-------CC-CTCCCGGCCTCCCGCCTCCG-------GGCGGGTCGG-CGCCCGCCGGAGG-ATAA-CCAAA----CTCT-GATT---TAACGACGTTTCTTCTGAGTGGTACAAGCAAATAATCA
Glomerella_graminicola            TCGAGTT-ACCGCTCTACAACCCTTTGTGAAC-ATACCT--AACTGTTGCTTCGGCGGGC-AGGGGG----TCCCCC--CGGGGA------CGCCCTCCCGGCCCCGCCCCCCTAC-C----AGGGGACGTGGCGCCCGCCGGAGG-ATA--CCCAA----CTCT-ATTT---TAACGACGTTTCTTCTGAGTGGCACAAGCAAATAATTA
Hypocrea_rufa                     CCGAGTTTACAACTCCCAAACCCAATGTGAACCATACCA-AA-CTGTTGCCTCGGCGGG---G--------TCACGCC--------------CCGGGTGCGTCGCAGCCCCG-------------GAACCAGGCGCCCGCCGGAGGGACCAACCAAACTCTTTCTGTAGTCCCTCGCGGACGTTATTTTTACAGCTCTGAGCAAAAATTCA
'P2-6'                            CTGAGTT-TACGCTCTACAACCCTTTGTGAAC-ATACCTATAACTGTTGCTTCGGCGGGT-AGG-G-----TCTCCGC-----GA-------CC-CTCCCGGCCTCCCGCCTCCG-------GGCGGGTCGG-CGCCCGCCGGAGG-ATAA-CCAAA----CTCT-GATT---TAACGACGTTTCTTCTGAGTGGTACAAGCAAATAATCA
Saccharomyces_cerevisiae          TTTTGTTATAGGACTTAAAACCG-TT-T---CAATACAACACACTGTGGAGTTTTCATATCTTTGCAACTTTTTCTTT------------GGGCATTCGAGCAATCGGGGCCAGAG---------GTAACAAACACAAACAATTTTATTTATTCATTA--AATTT-TTGTCAAAAACAAGAATTTTCGTAACTGGAAATTTTAAAATATTA
;
END;

BEGIN CODONS;
CODONPOSSET * CodonPositions (CHARACTERS = 'ITS1 with P2-6') = 
		N: 1-211;
CODONPOSSET  CodonPositions (CHARACTERS = 'ITS1 with P2-6') = 
		N: 1-211;
END;