#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 September 20, 2025; 4:49 GMT

TreeBASE (cc) 1994-2008

Study reference:
Munkacsi A., Stoxen S., & May G. 2006. Domestication of maize, sorghum, and sugarcane
did not drive the divergence of their smut pathogens. Evolution, null.

TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S1692]

[ The following blocks are input data for analysis step 3340 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep3340;
        DIMENSIONS NTAX=6;
        TAXLABELS
            Pseudozyma_prolifica
            Sporisorium_reilianum
            Sporisorium_sorghi
            Ustilago_hordei
            Ustilago_maydis
            Ustilago_scitaminea
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M891]

	TITLE 'RPB1_Figure 2';
	LINK TAXA = TaxaForAnalysisStep3340;
	DIMENSIONS NCHAR=576;
	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      ]
[                                  .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .      ]
Pseudozyma_prolifica      ACCGTCACAGATCCCGTCTTTGACCAAATCGTTAAGGCCACCCGCGGCAGCAAAAAGCGTCGCTTCCAGCGCGTTTGGGAGTACTGCTCCAAGAAGATGATCTGCGAAGCTGACGATCCCAAGGATGAAGACGAGATGGGCTTTGACGAGCAGAACAAGCCCGGTCACGGTGGATGCGGTCGTGTACAGCCCAACATTCGTCGCGAGGGCCTCAAATTGTTCACCCAGTGGAAAAAGGGCAAGGGCGAGGACGAGGACGGCGAGGAGAA---CGCCATCGCTCAAGCCGAAAAGCGACCCCTGCCCGCTTCCGAAGCACACACCATCCTAAAAAAGATGTCGAGTCATGACATTGCCGTTCTTGGTCTGTCCGAAGAAAACGCCCGCCCCGACTGGATGGTCCTCACCGTACTTCCCGTCCCGCCACCGCCCGTCCGTCCCTCGGTGCAAGATGGAGGCGAGGACGATTTGACATACAAGCTCGCCGATGTCATCCGTGCCAACGCTACACTCAAAAAAATGGAACAAGAAGGAACTCCGGCGCACATCTTGGCCGACTTTGAGCAGCTTCTCCAG
Sporisorium_reilianum     GTCGTCACAGACCCCGTCTTTGACCAGATCGTCAAAGCGACGCGCGGCAGCAGGAAACGCCGCTTCCAGCGCGTATGGGAGTACTGCTCCAAAAAGATGGTCTGCGAGGCCGACGAGCCCAAGGAGGACGACGAGATGGGTTTCGAAGAGCAAGCCAAGCCTGGGCACGGAGGATGTGGACGTATCCAGCCCAACATCCGTCGCGAGGGTCTCAAGCTGTTCACGCAGTGGAAGAAGGGCAAGGGCGAGGACGAGGACGGCGAGGAGAA---CGCCATCGCACAGGCAGAGAAGCGGCCCCTGCCCGCATCAGAGGCGCACACCATCCTCAAAAAGATGTCGAGCGAGGACATCGCCGTCCTCGGTCTCTCGGAGGAGAACGCGCGTCCCGACTGGATGGTCTTGACCGTGCTTCCCGTGCCCCCTCCGCCCGTACGACCCTCGGTGCAAGACGGAGGTGAAGACGACTTGACGTACAAGCTGGCCGACGTCATCCGTGCCAACGCGACGCTCAAAAAGATGGAGCAGGAAGGAACACCCGCGCACATTCTCGCCGACTTTGAACAGCTGCTCCAG
Sporisorium_sorghi        GTCGTCACAGATCCCGTCTTTGACCAGATCGTCAAGGCGACGCGCGGCAGCAGAAAGCGCCGCTTCCAGCGCGTGTGGGAGTACTGCTCCAAGAAGATGGTCTGCGAGGCCGACGAGCCAAAGGACGACGACGAGATGGGCTTCGACGACCAGTCCAAGCCCGGTCACGGAGGATGTGGCCGTGTCCAGCCCAACATTCGTCGCGAGGGTCTCAAGCTTTTCACGCAGTGGAAGAAGGGCAAGGGCGAGGACGACGACGGCGACGAGAA---CGCCATCGCTCAGGCAGAGAAGCGTCCCTTGCCCGCATCAGAGGCACACACCATTCTCAAAAAGATGTCGAGCGAGGACATTGCCGTGCTCGGTCTGTCGGAGGAGAACGCGCGTCCCGACTGGATGGTCTTGACCGTGCTTCCCGTGCCCCCGCCTCCCGTGCGACCCTCGGTGCAAGATGGAGGTGAAGATGATTTGACGTACAAGCTGGCCGACGTTATCCGTGCCAACGCCACGCTCAAAAAGATGGAGCAGGAAGGAACACCCGCGCACATTCTCGCGGACTTTGAACAGCTGCTTCAG
Ustilago_hordei           CAGGTCACGGACCCCGTCTTTGATCAGATCGTCAAGGCGACGCGCGGCAGTCGAAAGCGTCGCTTCCAGCGTGTATGGGAGTACTGCTCCAAGAAGATGGTTTGCGAGGCCGATGATCCTAAGGAGGAAGACGAGATGGGCTTCGAAGAGCAGGCTAAACCCGGTCACGGAGGATGTGGACGTGTACAGCCCAACATTCGTCGCGAAGGTCTTAAGCTCTTCACACAGTGGAAAAAGGGAAAGGGCGAGGACGAAGAGGGCGAGGAGACATCCGGCATCGCGCAGGCAGAGAAGCGTCCCTTGCCTGCATCCGAGGCCCACACCATCCTCAAGAAGATGTCGAGCGAGGACATTGCCGTCCTCGGTCTTTCCGAGGAGAACGCGCGCCCGGACTGGATGATCTTGACCGTCATGCCTGTCCCACCCCCGCCTGTCAGACCTTCGGTGCAAGATGGAGGTGAAGATGATTTGACATACAAGCTGGCCGATGTCATTCGTGCCAACGCCACCCTCAAGAAGATGGAGCAGGAGGGTACACCCGCACACATTCTCGCCGACTTTGAGCAGTTGCTCCGA
Ustilago_maydis           ACCGTCACAGATCCCGTCTTTGACCAAATCGTTAAGGCCACCCGCGGCAGCAAAAAGCGTCGCTTCCAGCGCGTTTGGGAGTACTGCTCCAAGAAGATGATCTGCGAAGCTGACGATCCCAAGGATGAAGACGAGATGGGCTTTGACGAGCAGAACAAGCCCGGTCACGGTGGATGCGGTCGTGTACAGCCCAACATTCGTCGCGAGGGCCTCAAATTGTTCACCCAGTGGAAAAAGGGCAAGGGCGAGGACGAGGACGGCGAGGAGAA---CGCCATCGCTCAAGCCGAAAAGCGACCCCTGCCCGCTTCCGAAGCACACACCATCCTAAAAAAGATGTCGAGTCATGACATTGCCGTTCTTGGTCTGTCCGAAGAAAACGCCCGCCCCGACTGGATGGTCCTCACCGTACTTCCCGTCCCGCCACCGCCCGTCCGTCCCTCGGTGCAAGATGGAGGCGAGGACGATTTGACATACAAGCTCGCCGATGTCATCCGTGCCAACGCTACACTCAAAAAAATGGAACAAGAAGGAACTCCGGCGCACATCTTGGCCGACTTTGAGCAGCTTCTCCAG
Ustilago_scitaminea       GTCGTCACAGATCCCGTCTTTGACCAGATCGTAAAAGCGACGCGCGGCAGCAGGAAACGCCGCTTCCAACATGTATGGGAGTACTGCTCCAAAAAGATGGTTTGCGAGGCCGACGAGCCAAAGGAGGAAGACGAGATGGGTTTCGAAGAGCAGGCCAAGCCCGGTCACGGAGGATGTGGTCGCGTCCAACCCAACATCCGTCGCGAGGGTCTCAAGCTTTTCACGCAGTGGAAGAAGGGCAAGGGCGAGGACGAGGACGGCGAGGAGAC---CGCTATCGCTCAGGCCGAAAAGCGTCCCTTGCCCGCATCAGAGGCACACACCATCCTCAAAAAGATGTCGAGCGAGGACATTGCCGTTCTCGGCTTGTCGGAGGAAAATGCGCGTCCCGACTGGATGGTCTTGACCGTGCTTCCCGTGCCCCCGCCCCCGGTTCGACCCTCGGTGCAAGATGGAGGTGAGGATGATTTGACATACAAGCTGGCCGACGTCATCCGTGCCAACGCCACGCTCAAAAAGATGGAGCAGGAAGGCACACCCGCGCACATTCTCGCCGACTTTGAGCAGCTGCTCCAG
;
END;

BEGIN CODONS;
CODONPOSSET * CodonPositions (CHARACTERS = 'RPB1_Figure 2') = 
		N: 1-576;
CODONPOSSET  CodonPositions (CHARACTERS = 'RPB1_Figure 2') = 
		N: 1-576;
END;
[ The following blocks are output data for analysis step 3340 ]
BEGIN TREES;
      TITLE Tb8113;
      LINK TAXA = TaxaForAnalysisStep3340;
      TREE Fig._2_RPB1 = [&R] ((((Sporisorium_reilianum,Ustilago_scitaminea),Sporisorium_sorghi),(Ustilago_maydis,Pseudozyma_prolifica)),Ustilago_hordei);
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr4714]


END;