#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 June 13, 2026; 18:07 GMT

TreeBASE (cc) 1994-2008

Study reference:
Jones J.J., Nita M., & Naidu R.A. 2014. Occurence and distribution of Grapevine leafroll
associated virus-2, -3 and Grapevine fleck virus and species of mealybugs
in Virginia and mid-Atlantic vineyards. European Journal of Plant Pathology, .

TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S16141]

[ The following blocks are input data for analysis step 14180 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep14180;
        DIMENSIONS NTAX=9;
        TAXLABELS
            'Grapevine fleck virus AJ309022-Unknown-Italy'
            'Grapevine fleck virus GU372367-Chardonnay-USA'
            'Grapevine fleck virus GU372368-Chardonnay-USA'
            'Grapevine fleck virus GU372369-Chardonnay-USA'
            'Grapevine fleck virus GU372370-Chardonnay-USA'
            'Grapevine fleck virus GU372371-Chardonnay-USA'
            'Grapevine fleck virus KF417610-Chancellor-USA *'
            'Grapevine fleck virus KF417611-Albarino-USA *'
            'Grapevine red globe virus AF521977-GRGV Outgroup'
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M23315]

	TITLE Grapevine_fleck_virus_Replicase_sequences;
	LINK TAXA = TaxaForAnalysisStep14180;
	DIMENSIONS NCHAR=464;
	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    ]
[                                                             .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .    ]
'Grapevine fleck virus AJ309022-Unknown-Italy'       AACACAATCCAGAAGGATA-CGATCGCCTCCTCCATC--ATTGCCGCCCTCAACCCTTCCCTCACCTCCTCCCTCACCCTCTACCCCTACG-CGCTCCCCCCGCGC----TGGCC-CTCCGCCCTCAACCAAGCCGGCATCCCCGCCA----CTTCCTACGGCCACCAATCCCACCCCCACCCAATCCACAA-GACCATT--GAAACCCATCTCCTCCATGAGCATTGGGCCAACCGTGCGACTCTCCCGTCCACGGTCATG-TTCATGAAGAGGTCGAAGTT---CGACAAGCTCCGC------GTCTCCAACGCGGCTCTCGTCAAATCGGCCTCAAACTTCC--TCCACCTCCTCAACCCCATCCTCACCGCCCGGGACG---CCGACCGGTACACCCAC-CTCCCCCTCCCCGACACCCTCCCCTCCACCCCTCTCTACTTCATG-CATC-ATTCCCTCA
'Grapevine fleck virus GU372367-Chardonnay-USA'      AACACCATCCAGAAGGACA-CGATCGCCTCATCCATC--ATCGCCGCCCTTAACCCTTCCCTCACCTCCTCCCTCACCCTCTACCCCTACG-CGCTCCCCTCGCGT----TGGCC-CTCCGCCCTCAACCAAGCTGGCATTCCTGCCA----CTTCCTACGGCCACCAATCCCACCCTCACCCAATCCACAA-GACCATC--GAAACCCATCTCCTTCATGAGCATTGGGCCAACCGTGCGACTCTCCCGTCCACGGTTATG-TTCATGAAGAGGTCGAAGTT---CGACAAGCTCCGT------GTCTCCAACGCGGCGCTCGTCAAATCGGCCTCAAACTTCC--TTCACCTCCTCAACCCCATCCTCACCGCCCGGGACG---CCGACCGGTACACCCAC-CTCCCCCTCCCCGACACCCTCCCCTCCACCCCTCTCTACTTCATG-CATG-ATGCCCTCA
'Grapevine fleck virus GU372368-Chardonnay-USA'      AACACCATCCAGAAGGACA-CGATCGCCTCGTCCATC--ATCGCGGCCCTCAACCCATCCCTCACCTCATCCCTCACTCTCTATCCCTACG-CGCTCCCCGCGCGT----TGGCC-CGCAGCCCTCAACCACGCCGGCATCCCCGCCA----CCTCCTATGGCCACCAATCCCACCCCCACCCCATCCATAA-GACCATC--GAAACCCACCTCCTTCACGAACACTGGGCTAACCGTGCCACCCTCCCCTCCACGGTCATG-TTCATGAAGCGATCCAAGTT---TGACAAGCTCCGC------GTCTCCAACGCGGCGCTCGTCAAATCGGCCTCAAACTTCC--TCCACCTCCTCAACCCCATTCTTACCGCTCGCGACG---CCGATCGGTACACCCAC-ATGCCCCTTCCCGAATCCCTTCCCTCCACTCCCCTCTACTTCATG-CATG-ACGCCCTCA
'Grapevine fleck virus GU372369-Chardonnay-USA'      AACACCATCCAGAAGGACA-CGATCGCCTCATCCATC--ATCGCCGCCCTTAACCCTTCCCTCACCTCCTCCCTCACCCTCTACCCCTACG-CGCTCCCCTCGCGT----TGGCC-CTCCGCCCTCAACCAAGCTGGCATTCCTGCCA----CTTCCTACGGCCACCAATCCCACCCCCACCCAATCCACAA-GACCATC--GAAACCCATCTCCTTCATGAGCATTGGGCCAACCGTGCGACTCTCCCGTCCACGGTCATG-TTCATGAAGAGGTCGAAGTT---CGACAAGCTCCGT------GTCTCCAACGCGGCGCTCGTCAAATCGGCCTCAAACTTCC--TTCACCTCCTCAACCCCATCCTCACCGCCCGGGACG---CCGACCGGTACACCCAC-CTCCCCCTCCCCGACACCCTCCCCTCCACCCCTCTCTACTTCATG-CATG-ACGCCCTCA
'Grapevine fleck virus GU372370-Chardonnay-USA'      AACACCATCCAGAAGGACA-CGATCGCCTCATCCATC--ATCGCCGCCCTTAACCCTTCCCTCACCTCCTCTCTTACCCTCTACCCCTACG-CGCTCCCCTCGCGT----TGGCC-CTCCGCCCTCAACCAAGCTGGCATTCCTGCCA----CTTCCTACGGCCACCAATCCCACCCCCACCCAATCCACAA-GACCATC--GAAACCCATCTCCTTCATGAGCATTGGGCCAACCGTGCGACTCTCCCGTCCACGGTCATG-TTCATGAAGAGGTCGAAGTT---CGACAAGCTCCGT------GTCTCCAACGCGGCGCTCGTCAAATCGGCCTCAAACTTCC--TTCACCTCCTCAACCCCATCCTCACCGCCCGGGACG---CCGACCGGTACACCCAC-CTCCCCCTCCCCGACACCCTCCCCTCCACCCCTCTCTACTTCTTG-CATG-ATGCCCTCA
'Grapevine fleck virus GU372371-Chardonnay-USA'      AACACCATCCAGAAGGACA-CGATCGCCTCCTCCATC--ATCGCCGCCCTTAACCCTTCCCTCACCTCCTCCCTCACCCTCTACCCCTACG-CGCTCCCCTCGCGC----TGGCC-CTCCGCCCTCAACCAAGCCGGCATCCCCGCCA----CTTCCTACGGCCACCAATCCCACCCCCACCCCATCCACAA-GACCATC--GAAACCCATCTCCTTCATGAGCATTGGGCCAACCGTGCGACTCTCCCGTCCACGGTCATG-TTCATGAAGAGGTCGAAGTT---CGACAAGCTCCGT------GTCTCCAACGCGGCGCTCGTCAAATCGGTCTCAAACTTCC--TTCACCTCCTCAACCCCATCCTCACCGCCCGGGACG---CCGACCGGTACACCCAC-CTCCCCCTCCCCGACACCCTCCCCTCCACCCCTCTCTACTTCATG-CATG-ATGCCCTCA
'Grapevine fleck virus KF417610-Chancellor-USA *'    AACACCATCCAGAAGGACA-CGATCGCCTCCTCCATC--ATAGCCGCTCTCAACCCCTCCCTCACCTCCTCTCTCACCCTCTATCCCTACG-CCCTCCCGGCGCGT----TGGCC-GTCCGCGCTCAACCACGCCGGAATCCCTGCCA----CCTCCTACGGCCACCAATCCCATCCTCACCCCATCCATAA-GACCATT--GAAACCCATCTCCTCCATGAGCACTGGGCTAACCGCGCCACCCTCCCTTCCACCGTCCTG-TTCATGAAGAGGTCGAAGTT---TGACAAGCTCCGG------GTCTCCAACGCGGCGCTCGTCAAATCGGCCTCAAACTTCC--TTCACCTCCTCAACCCCATCCTCACCGCCCGTGACG---CCGACCGTTACACCCAC-ATGCCCCTCCCCGACACCCTCCCGTCAACCCCCCTCTACTTCATG-CATG-ACGCCCTCG
'Grapevine fleck virus KF417611-Albarino-USA *'      AAGAGTGTCTGGAAGGACA-CGATCGCGTCTTCCATC--ATCGCCGCCCTTAACCCTTCCCTCACCTCCTCCCTCACCCTCTACCCCTACG-CGCTCCCCTCGCGC----TGGCC-TTCCGCCCTCAACCAAGCCGGCATCCCTGCCA----CTTCCTACGGCCACCAATCCCACCCCCACCCCATCCACAA-GACCATC--GAAACCCATCTCCTTCATGAGCATTGGGCCAACCGCGCGACTCTCCCGTCCACGGTCATG-TTCATGAAGAGGTCGAAGTT---CGACAAGCTCCGT------GTCTCCAACGCGGCGCTCGTCAAATCGGCCTCAAACTTCC--TCCACCTCCTCAACCCCATCCTCACCGCCCGGGACG---CCGACCGGTACACCCAC-CTTCCCCTCCCCGACACCCTCCCTTCCACCCCTCTCTATTTCATG-CATG-ATGCCCTCA
'Grapevine red globe virus AF521977-GRGV Outgroup'   TCCATCCCTCAGCCCCTCATCGATCTCCACGTGCATCTGAAGACCAACGTGGACACCCAACTCGGCCCCCTCACCTCCATGCGCCTCACTGGCGAACCAGGAACGTATGATGACAACTCTGATTACAACCTGGCCGTCACTGCAGCCAAATTCATCCTA-GACCCCGAGGTCCACGCCGTTCTCATCTCCGGCGACGATCTTGACATCTCCCCCCCCCCTCCAGTCCGCCCCACCTGGCCCATTCTCGAAGCCATGCTCTCACTTCGCTTCAAGACTGAAGTCTCCCGCTACGGTCTTTTCTGCGGTTACTATCTTGGCCCCGCTGGAGCCGTCCGCTCACCTCTGGCCCTCTTTGCCAAGCTCATCATCGCCGTCGACGACGGTTCCATCGAGGACAAGAAAGCTTCATATCTCTCAGAATTTGCTGTCGGCCACTCCCTCGGTCAGGACATGTGGACTCTC-
;
END;

[ The following blocks are output data for analysis step 14180 ]
BEGIN TREES;
      TITLE Grapevine_fleck_virus_Replicase_ML_analysis_tree;
      LINK TAXA = TaxaForAnalysisStep14180;
      TREE Imported_tree_0 = [&R] ((('Grapevine fleck virus GU372368-Chardonnay-USA','Grapevine fleck virus KF417610-Chancellor-USA *')0.8050,'Grapevine fleck virus AJ309022-Unknown-Italy','Grapevine fleck virus KF417611-Albarino-USA *','Grapevine fleck virus GU372371-Chardonnay-USA',('Grapevine fleck virus GU372369-Chardonnay-USA',('Grapevine fleck virus GU372367-Chardonnay-USA','Grapevine fleck virus GU372370-Chardonnay-USA')0.7500)0.7070),'Grapevine red globe virus AF521977-GRGV Outgroup');
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr76539]


END;