#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 25, 2024; 1:30 GMT

TreeBASE (cc) 1994-2008

Study reference:
Peever T., Su G., Carpenter-boggs L., & Timmer L. 2003. Molecular systematics of
citrus-associated Alternaria species. Mycologia, 96(1): 119-134.

TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S1002]

BEGIN TAXA;
        TITLE  'beta-tubulin';
        DIMENSIONS NTAX=16;
        TAXLABELS
            Alternaria_alternata_1
            Alternaria_alternata_2
            Alternaria_arbusti
            Alternaria_brassicicola
            Alternaria_citri
            Alternaria_citri_UC4s
            Alternaria_conjuncta
            Alternaria_gaisen
            Alternaria_infectoria
            Alternaria_limicola_1
            Alternaria_limicola_2
            Alternaria_longipes
            Alternaria_solani_5
            Alternaria_solani_8
            Alternaria_toxicogenica
            Alternaria_turkisafria
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M566]

	TITLE 'beta-tubulin';
	LINK TAXA = 'beta-tubulin';
	DIMENSIONS NCHAR=374;
	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    ]
[                                    .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .    ]
Alternaria_alternata_1      GTCAAACGTCCCTG-CGGCGCGTC-CTGCCCCGCGCCTAGA--TATCATT-CAGGGACA----AGCGCGAACAACAGAGAACAACAGCTAACAACTCTTCTGTGCAACAGGTTCACCTCCAGACCGGTCAATGCGTAAGCTCT--TCTCTCCTC-----AAACATCCAGACGACAGCTAATAGTGTTTTC-AGGGTAACCAAATCGGTGCTGCCTTTTGGCAGACCATCTCCGGCGAGCATGGCCTCGACGGCCCTAGTGTCTACAACGGCACTTCAGACCTCCAGTTGGAGCGCATGAACGTCTACTTCAACGAAGTACGTCACTCGATATTCCATACGGCAGATAAAAGGCCAATACTGATCTATAGCAGGC
Alternaria_alternata_2      GTCAAACGTCCCTG-TGGCGCGTC-CTGCCCCGCGCCTAGA--TATCATT-CAGGGACA----AGCGCGAACAACAGAGAACAACAGCTAACAACTCTTCTGTGCAACAGGTTCACCTCCAGACCGGTCAATGCGTAAGCTCT--TCACTCCTC-----AAACATCCAGACGACAGCTAATAGTGTTTTC-AGGGTAACCAAATCGGTGCTGCCTTTTGGCAGACCATCTCCGGCGAGCATGGCCTCGACGGCTCTGGTGTCTACAACGGCACTTCAGACCTCCAGTTGGAGCGCATGAACGTCTACTTCAACGAAGTACGTCACTCGATATTCCATACGGCAGATAAAAGGCCAATACTGATCTATAGCAGGC
Alternaria_arbusti          -TGCCGCCTAGTGG-TGGCGCGTCGCTGCCCCGCGCCGAGA------CTC--AGGGACA-----ACATAAAGAAC-------AACAGCTAACGACGTTTCT-TGCAACAGGTTCACCTTCAGACCGGTCAATGCGTAAGTTTTGATATCGCTCCT----CTGT--ACAGACGACAGCTAACAT---TGCCCAGGGTAACCAAATCGGTGCCGCCTTCTGGCAGACCATCTCCGGCGAGCATGGCCTCGACGGCTCCGGTGTCTACAACGGCACCTCGGACCTGCAGCTCGAGCGCATGAATGTCTACTTCAACGAAGTGCGTCCCCCGATTACGCTTTTGGCAGATAAAAGACCAATACTGATCTACAGCAGGC
Alternaria_brassicicola     TTAAGAAGTCGCTG-TGGCGCGTCGCTGCCCCGCGCCTAGAAGTAGCATTTCAGGGACACACAAGCGCGAACAATAGAGAACAACAGCTAACGGCGTTTCT-TGCAACAGGTCCACCTCCAGACCGGTCAATGTGTAAGCTCTCGTCGCTCCTCTACATGAAAACGACAACAGCAACTAACAGC-CTCTC-AGGGTAACCAGATCGGTGCTGCCTTCTGGCAGACCATCTCCGGCGAGCATGGCCTCGACGGCTCGGGTGTCTACAACGGCACTTCAGACCTCCAGCTGGAGCGCATGAACGTCTACTTCAACGAAGTACGTCACTCGATACTCGATACGCCAGATAAAAGGCCAATACTGATCTATAGCAGGC
Alternaria_citri            GTCAAACGTCCCTG-TGGCGCGTC-CTGCCCCGCGCCTAGA--TATCATT-CAGGGACA----AGCGCGAACAACAGAGAACAACAGCTAACAACTCTTCTGTGCAACAGGTTCACCTCCAGACCGGTCAATGCGTAAGCTCT--TCTCTCCTC-----AAACATCCAGACGACAGCTAATAGTGTTTTC-AGGGTAACCAAATCGGTGCTGCCTTTTGGCAGACCATCTCCGGCGAGCATGGCCTCGACGGCTCTGGTGTCTACAACGGCACTTCAGACCTCCAGTTGGAGCGCATGAACGTCTACTTCAACGAAGTACGTCACTCGATATGCCATACGGCAGATAAAAGGCCAATACTGATCTATAGCAGGC
Alternaria_citri_UC4s       GTCAAACGTCCCTG-TGGCGCGTC-CTGCCCCGCGCCTAGA--TATCATT-CAGGGACA----AGCGCGAACAAC--A--------GCTAACAACTCTTCTGTGCAACAGGTTCACCTCCAGACCGGTCAATGCGTAAGCTCT--TCTCTCCTC-----AAACATCCAGACGATAGCTAATAGTGTTTTC-AGGGTAACCAAATCGGTGCTGCCTTTTGGCAGACCATCTCCGGCGAGCATGGCCTCGACGGCTCTGGTGTCTACAACGGCACTTCAGACCTCCAGTTGGAGCGCATGAACGTCTACTTCAACGAAGTACGTCACTCGATATTCCATACGGCAGATAAAAGGCCAATACTGATCTATAGCAGGC
Alternaria_conjuncta        -TGCCGCCTAGTCG-TGGCGCGTCGCTGCCCCGCGCCGAGA------CTC--AGGGACA-----ACACAAAGAAC-------AACAGCTAACGACGATTCTCTGCAACAGGTGCACCTTCAGACCGGTCAATGCGTAAGTCTACATATCGCTCCT----CTGT--ACAGACGACAGCTAACA----CCCCCAGGGTAACCAAATCGGTGCCGCCTTCTGGCAGACCATTTCCGGCGAGCATGGCCTCGACGGCTCCGGTGTCTACAACGGCACCTCGGACCTGCAGCTCGAGCGCATGAACGTCTACTTCAACGAAGTGCGTCCCCCGATTACGCTTTTGGCAGATAAAAGACCAATACTGATCCACAGCAGGC
Alternaria_gaisen           GTCAAACGTCCCTG-TGGCGCGTC-CTGCCCCGCGCCTAGA--TATCATT-CAGGGACA----AGCGCGAACAATAGAGAACAACAGCTAACAACTCTTCTGTGCAACAGGTTCACCTCCAGACCGGTCAATGCGTAAGCTCT--TCTCTCCTC-----AAACATCCAGACGACAGCTAATAGTGTTTTC-AGGGTAACCAAATCGGTGCTGCCTTTTGGCAGACCATCTCCGGCGAGCATGGCCTCGACGGCTCTGGTGTCTACAACGGCACTTCAGACCTCCAGTTGGAGCGCATGAACGTCTACTTCAACGAAGTACGTCACTCGATATTCCATACGGCAGATAAAAGGCCAATACTGATCTATAGCAGGC
Alternaria_infectoria       -TGCCGCCTAGTCG-TGGCGCGTCGCTGCCCCGCGCCGAGA------CTC--AGGGACA-----ACACAAAGAAC-------AACAGCTAACGACGTTTCTCTGCCACAGGTTCACCTTCAGACCGGTCAATGCGTAAGTTTTGATATCGCTCCT----CTGTGTACAGACGACAGCTAACAA---TCTCCAGGGTAACCAAATCGGTGCCGCCTTCTGGCAGACCATCTCCGGCGAGCATGGCCTCGACGGCTCCGGTGTCTACAACGGCACCTCGGACCTGCAGCTCGAGCGCATGAATGTCTACTTCAACGAAGTGCGTCCCTCGATTACGCTTTTGGCAGATAAAAGACCAATACTGATCTACAGCAGGC
Alternaria_limicola_1       CTGCGGCGTCGCCGGTGGCGCGTC-GTGCCCCGCGCCCACA--TATCATT-CAGGGACA----CGCGCCCGCAAGGGACAACATCAGCTAACACGTCTTGCTTGCAACAGGTTCACCTTCAGACCGGCCAATGCGTAAGCTCTCCTCGCGTCCCCTCG-AGCCGCCCGGGCGACAGCTAACAGTGTTTTCCAGGGTAACCAAATTGGTGCTGCCTTCTGGCAGACCATTTCCGGCGAGCATGGTCTCGACGGCTCTGGTGTCTACAACGGCACGTCAGACCTCCAGCTGGAGCGCATGAACGTCTACTTCAACGAAGTACGTCGCCCGATACTCGGTACGGCAGATAAAAGACCAATACTGATCTACAGCAGGC
Alternaria_limicola_2       CTGCGGCGTCGCCGGTGGCGCGTC-GTGCCCCGCGCCCACA--TATCATT-CAGGGACA----CGCGCCCGCAAGGGACAACATCAGCTAACACGTCTTGCTTGCAACAGGTTCACCTTCAGACCGGCCAATGCGTAAGCTCTCCTCGCGTCCCCTCG-AGCCGCCCGGGCGACAGCTAACAGTGTTTTCCAGGGTAACCAAATTGGTGCTGCCTTCTGGCAGACCATTTCCGGCGAGCATGGTCTCGACGGCTCTGGTGTCTACAACGGCGCGTCAGACCTCCAGCTGGAGCGCATGAACGTCTACTTCAACGAAGTACGTCGCCCGATACTCGGTACGGCAGATAAAAGACCAATACTGATCTACAGCAGGC
Alternaria_longipes         GTCAAACGTCCCTG-TGGCGCGTC-CTGCCCCGCGCCTAGA--TATCATT-CAGGGACA----AGCGCGAACAACAGAGGACGACAGCTAACAACTCTTCTGTGCAACAGGTTCACCTCCAGACCGGTCAATGCGTAAGCTCT--TCTCTCCTC-----AAACATCCAGACGACAGCTAATAGTGTTTTC-AGGGTAACCAAATCGGTGCTGCCTTTTGGCAGACCATCTCCGGCGAGCATGGCCTCGACGGCTCTGGTGTCTACAACGGCACTTCAGACCTCCAGTTGGAGCGCATGAACGTCTACTTCAACGAAGTACGTCACTCGATATTCCATACGGCAGATAAGAGGCCAATACTGATCTATAGCAGGC
Alternaria_solani_5         TGCCCACGTCCCTGGTGGCGCGTC-GTGCCCCGCGCCGAGA--TATTATT-CAGGGACA----CGCGCGAACAAGGGAGAACAACAGCTAACACGTCTTGCTTGCAACAGGTTCACCTTCAGACCGGTCAACGCGTAAGTTGTCCTCTCATCTCCTCC-AGCCGCCCAGACGACAGCTAACAGTATTTTC-AGGGTAACCAAATTGGTGCTGCCTTCTGGCAGACCATTTCCGGCGAGCATGGCCTCGACGGCTCTGGTGTCTACAACGGCACTTCAGACCTCCAGCTGGAGCGCATGAACGTCTACTTCAACGAAGTACGTCACCCGATATTGGATACGGCAGATAAAAGACCAATACTGATCTGTAGCAGGC
Alternaria_solani_8         TGCCCACGTCCCTGGTGGCGCGTC-GTGCCCCGCGCCGAGA--TATTATT-CAGGGACA----CGCGCGAACAAGGGAGAACAACAGCTAACACGTCTTGCTTGCAACAGGTTCACCTTCAGACCGGTCAATGCGTAAGTCCTCCTCTCGTCCTCTCC-AGCCGCCCAGACGACAGCTAACAGTATTTTC-AGGGTAACCAAATTGGTGCTGCCTTCTGGCAGACCATTTCCGGCGAGCATGGCCTCGACGGCTCTGGTGTCTACAACGGCACTTCAGACCTCCAGCTGGAGCGCATGAACGTCTACTTCAACGAAGTACGTCACCCGATATTCGATACGGCAGATAAAAGACCAATACTGATCTGTAGCAGGC
Alternaria_toxicogenica     GTCAAACGTCCCTG-TGGCGCGTC-CTGCCCCGCGCCTAGA--TATCATT-CAGGGACA----AGCGCGAACAACAGAGAACAACAGCTAACAACTCTTCTGTGCAACAGGTTCACCTCCAGACCGGTCAATGCGTAAGCTCT--TCTCTCCTC-----AAACATCCAGACGACAGCTAATAGTGTTTTC-AGGGTAACCAAATCGGTGCTGCCTTTTGGCAGACCATCTCCGGCGAGCATGGCCTCGACGGCTCTGGTGTCTACAACGGCACTTCAGACCTCCAGTTGGAGCGCATGAACGTCTACTTCAACGAAGTACGTCACTCGATATTCCATACGGCAGATAAAAGGCCAATACTGATCTATAGCAGGC
Alternaria_turkisafria      GTCAAACGTCCCTG-TGGCGCGTC-CTGCCCCGCGCCTAGA--TATCATT-CAGGGACG----AGCGCGAACAACAGAGAACAACAGCTAACAACTCTTCTGTGCAACAGGTTCACCTCCAGACCGGTCAATGCGTAAGCTCT--TCTCTCCTC-----AAACATCCAGACGACAGCTAATAGTGTTTTC-AGGGTAACCAAATCGGTGCTGCCTTTTGGCAGACCATCTCCGGCGAGCATGGCCTCGACGGCTCTGGTGTCTACAACGGCACTTCAGACCTCCAGTTGGAGCGCATGAACGTCTACTTCAACGAAGTACGTCACTCGATATTCCATACGGCAGATAAAAGGTCAATACTGATCTATAGCAGGC
;
END;

BEGIN CODONS;
CODONPOSSET * CodonPositions (CHARACTERS = 'beta-tubulin') = 
		N: 1-374;
CODONPOSSET  CodonPositions (CHARACTERS = 'beta-tubulin') = 
		N: 1-374;
END;