#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 13, 2024; 3:35 GMT

TreeBASE (cc) 1994-2008

Study reference:
Van poucke K., Franceschini S., Webber J.F., Vercauteren A., Judith T., Mccracken
A.R., Heungens K., & Brasier C. 2012. Discovery of a fourth evolutionary lineage
of Phytophthora ramorum: EU2. Fungal Biology, 116(11): 1178-1191.

TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S12540]

[ The following blocks are input data for analysis step 8870 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep8870;
        DIMENSIONS NTAX=9;
        TAXLABELS
            Phytophthora_hibernalis
            Phytophthora_lateralis
            Phytophthora_ramorum_EU1a
            Phytophthora_ramorum_EU1b
            Phytophthora_ramorum_EU2
            Phytophthora_ramorum_NA1a
            Phytophthora_ramorum_NA1b
            Phytophthora_ramorum_NA2a
            Phytophthora_ramorum_NA2b
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M14322]

	TITLE alignment_Btub;
	LINK TAXA = TaxaForAnalysisStep8870;
	DIMENSIONS NCHAR=908;
	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       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900        ]
[                                      .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .        ]
Phytophthora_hibernalis       CGACGTCGTCCGCAAGGAGGCTGAGAGCTGTGACTGCCTGCAAGGGTTCCAGATCACGCACTCGCTCGGTGGCGGTACCGGCTCCGGAATGGGCACGCTCCTGATCTCCAAGATCCGTGAGGAGTACCCGGACCGTATCATGTGCACATACTCCGTGTGCCCGTCGCCCAAGGTGTCGGACACCGTCGTGGAGCCCTACAACGCCACACTGTCGGTGCACCAGCTTGTCGAGAACGCTGATGAGGTCATGTGCCTGGATAACGAGGCGCTGTACGACATTTGCTTCCGTACGCTCAAGCTCACCACCCCCACGTACGGTGACCTGAACCACCTGGTGTGTGCCGCCATGTCCGGCATCACCACGTGCCTGCGGTTCCCCGGTCAGCTGAACTCGGACCTGCGGAAACTGGCCGTGAACCTGATCCCGTTCCCGCGTCTTCACTTCTTCATGATTGGCTTCGCCCCGCTGACCTCGCGTGGCTCGCAGCAGTACCGTGCCCTGACGGTGCCCGAGCTCACCCAGCAGCAGTTCGACGCTAAGAACATGATGTGCGCCGCCGACCCTCGCCACGGCCGCTATTTAACTGCCGCGTGTATGTTCCGCGGACGTATGAGCACGAAGGAGGTGGATGAGCAGATGCTCAACGTGCAGAACAAGAACTCGTCGTACTTCGTCGAGTGGATCCCTAACAACATCAAGGCTAGCGTGTGTGACATCCCGCCCAAGGGACTCAAGATGAGTACCACGTTCATCGGTAACTCGACCGCTATCCAGGAAATGTTCAAGCGTGTGTCTGAGCAGTTTACGGCAATGTTCCGTCGTAAGGCTTTCTTGCACTGGTACACGGGCGAGGGTATGGACGAGATGGAGTTCACGGAGGCCGAGTCCAACATGAATGATCTTGTGT
Phytophthora_lateralis        TGACGTCGTCCGCAAGGAGGCCGAGAGCTGTGACTGCCTGCAGGGGTTCCAGATCACGCACTCGCTGGGTGGCGGTACCGGTTCCGGTATGGGCACGCTTCTGATCTCCAAGATCCGTGAGGAGTACCCGGACCGTATCATGTGCACGTACTCGGTGTGCCCGTCGCCCAAGGTGTCGGACACTGTCGTGGAGCCCTACAACGCCACGCTGTCAGTGCACCAGCTTGTCGAGAACGCCGATGAGGTCATGTGCCTGGATAACGAGGCCCTGTACGACATCTGCTTCCGCACGCTCAAGCTCACCACCCCCACCTACGGTGACCTGAACCACCTCGTGTGCGCAGCAATGTCCGGCATCACCACATGCCTGCGTTTCCCGGGTCAGCTGAACTCGGACCTGCGGAAGCTGGCGGTGAACCTGATTCCGTTCCCGCGTCTTCACTTCTTCATGATTGGTTTCGCCCCGCTGACTTCGCGTGGCTCGCAGCAGTACCGTGCCCTGACGGTGCCTGAGCTGACCCAGCAGCAGTTCGACGCAAAGAACATGATGTGCGCCGCCGACCCTCGTCACGGCCGCTATTTAACTGCCGCGTGTATGTTCCGCGGACGTATGAGCACGAAGGAGGTTGATGAGCAGATGCTGAACGTGCAGAACAAGAACTCGTCGTACTTCGTCGAGTGGATCCCTAACAACATCAAGGCTAGCGTGTGTGACATCCCGCCCAAGGGGCTGAAGATGAGCACCACGTTCATCGGTAACTCGACCGCTATCCAGGAGATGTTCAAGCGTGTGTCTGAGCAGTTTACGGCAATGTTCCGTCGTAAGGCTTTCTTGCACTGGTACACGGGCGAGGGTATGGACGAGATGGAGTTCACTGAGGCCGAGTCCAACATGAATGATCTTGTGT
Phytophthora_ramorum_EU1a     CGACGTCGTCCGCAAGGAGGCCGAGAGCTGTGACTGCCTGCAGGGGTTCCAGATCACGCACTCGCTTGGTGGCGGTACCGGTTCTGGTATGGGCACGCTTCTGATCTCCAAGATCCGTGAGGAGTACCCGGACCGTATCATGTGCACGTACTCGGTGTGCCCGTCGCCCAAGGTGTCGGACACGGTCGTGGAGCCCTACAACGCCACGCTGTCGGTGCACCAGCTTGTCGAGAACGCCGACGAGGTCATGTGCCTGGATAACGAGGCGCTGTACGACATTTGCTTCCGCACGCTCAAGCTCACCACCCCCACCTACGGTGACCTGAACCACCTGGTGTGCGCCGCTATGTCCGGCATCACCACGTGCCTGCGTTTCCCGGGTCAGCTGAACTCGGACCTGCGGAAGCTGGCGGTGAACTTGATTCCGTTCCCGCGTCTTCACTTCTTCATGATTGGTTTCGCCCCGCTGACCTCGCGTGGCTCGCAGCAGTACCGTGCCCTGACGGTGCCCGAGCTGACCCAGCAGCAGTTCGACGCAAAGAACATGATGTGCGCCGCCGACCCTCGTCACGGCCGCTATTTAACTGCCGCGTGTATGTTCCGCGGACGTATGAGCACGAAGGAGGTTGACGAGCAGATGCTGAACGTGCAGAACAAGAACTCGTCGTACTTCGTCGAGTGGATCCCTAACAACATCAAGGCTAGCGTGTGTGACATCCCGCCCAAGGGGCTGAAGATGAGCACTACGTTCATCGGTAACTCGACCGCTATCCAGGAGATGTTCAAGCGTGTGTCTGAGCAGTTTACGGCTATGTTCCGTCGTAAGGCTTTCTTGCACTGGTACACGGGCGAGGGTATGGACGAGATGGAGTTCACGGAGGCCGAGTCCAACATGAATGATCTTGTGT
Phytophthora_ramorum_EU1b     CGACGTCGTCCGCAAGGAGGCCGAGAGCTGTGACTGCCTGCAGGGGTTCCAGATCACGCACTCGCTTGGTGGCGGTACCGGTTCTGGTATGGGCACGCTTCTGATCTCCAAGATCCGTGAGGAGTACCCGGACCGTATCATGTGCACGTACTCGGTGTGCCCGTCGCCCAAGGTGTCGGACACGGTCGTGGAGCCCTACAACGCCACGCTGTCGGTGCACCAGCTTGTCGAGAACGCCGACGAGGTCATGTGCCTGGATAACGAGGCGCTGTACGACATTTGCTTCCGCACGCTCAAGCTCACCACCCCCACCTACGGTGACCTGAACCACCTGGTGTGCGCCGCTATGTCCGGCATCACCACGTGCCTGCGTTTCCCGGGTCAGCTGAACTCGGACCTGCGGAAGCTGGCGGTGAACTTGATTCCGTTCCCGCGTCTTCACTTCTTCATGATTGGTTTCGCCCCGCTGACCTCGCGTGGCTCGCAGCAGTACCGTGCCCTGACGGTGCCCGAGCTGACCCAGCAGCAGTTCGACGCAAAGAACATGATGTGCGCCGCCGACCCTCGTCACGGCCGCTATTTAACTGCCGCGTGTATGTTCCGCGGACGTATGAGCACGAAGGAGGTTGATGAGCAGATGCTGAACGTGCAGAACAAGAACTCGTCGTACTTCGTCGAGTGGATCCCTAACAACATCAAGGCTAGCGTGTGTGACATCCCGCCCAAGGGCCTGAAGATGAGCACTACGTTCATCGGTAACTCGACCGCTATCCAGGAGATGTTCAAGCGTGTGTCTGAGCAGTTTACGGCTATGTTCCGTCGTAAGGCTTTCTTGCACTGGTACACGGGCGAGGGTATGGACGAGATGGAGTTCACGGAGGCCGAGTCCAACATGAACGATCTTGTGT
Phytophthora_ramorum_EU2      CGACGTCGTCCGCAAGGAGGCCGAGAGCTGTGACTGCCTGCAGGGGTTCCAGATCACGCACTCGCTGGGTGGCGGTACCGGTTCTGGTATGGGCACGCTTCTGATCTCCAAGATCCGTGAGGAGTACCCGGACCGTATCATGTGCACGTACTCGGTGTGCCCGTCGCCCAAGGTGTCGGACACGGTCGTGGAGCCCTACAACGCCACGCTGTCGGTGCACCAGCTTGTCGAGAACGCCGACGAGGTCATGTGCCTGGATAACGAGGCGCTGTACGACATTTGCTTCCGCACGCTCAAGCTCACCACCCCCACCTACGGTGACCTGAACCACCTGGTGTGCGCCGCTATGTCCGGCATCACCACGTGCCTGCGTTTCCCGGGTCAGCTGAACTCGGACCTGCGGAAGCTGGCGGTGAACTTGATTCCGTTCCCGCGTCTTCACTTCTTCATGATTGGTTTCGCCCCGCTGACCTCGCGTGGCTCGCAGCAGTACCGTGCCCTGACGGTGCCCGAGCTGACCCAGCAGCAGTTCGACGCAAAGAACATGATGTGCGCCGCCGACCCTCGTCACGGCCGCTATTTAACTGCCGCGTGTATGTTCCGCGGACGTATGAGCACGAAGGAGGTTGATGAGCAGATGCTGAACGTGCAGAACAAGAACTCGTCGTACTTCGTCGAGTGGATCCCTAACAACATCAAGGCTAGCGTGTGTGACATCCCGCCCAAGGGCCTGAAGATGAGCACTACGTTCATCGGTAACTCGACCGCTATCCAGGAGATGTTCAAGCGTGTGTCTGAGCAGTTTACGGCTATGTTCCGTCGTAAGGCTTTCTTGCACTGGTACACGGGCGAGGGTATGGACGAGATGGAGTTCACGGAGGCCGAGTCCAACATGAACGATCTTGTGT
Phytophthora_ramorum_NA1a     CGACGTCGTCCGCAAGGAGGCCGAGAGCTGTGACTGCCTGCAGGGGTTCCAGATCACGCACTCGCTTGGTGGCGGTACCGGTTCTGGTATGGGCACGCTTCTGATCTCCAAGATCCGTGAGGAGTACCCGGACCGTATCATGTGCACGTACTCGGTGTGCCCGTCGCCCAAGGTGTCGGACACGGTCGTGGAGCCCTACAACGCCACGCTGTCGGTGCACCAGCTTGTCGAGAACGCCGACGAGGTCATGTGCCTGGATAACGAGGCGCTGTACGACATTTGCTTCCGCACGCTCAAGCTCACCACCCCCACCTACGGTGACCTGAACCACCTGGTGTGCGCCGCTATGTCCGGCATCACCACGTGCCTGCGTTTCCCGGGTCAGCTGAACTCGGACCTGCGGAAGCTGGCGGTGAACTTGATTCCGTTCCCGCGTCTTCACTTCTTCATGATTGGTTTCGCCCCGCTGACCTCGCGTGGCTCGCAGCAGTACCGTGCCCTGACGGTGCCCGAGCTGACCCAGCAGCAGTTCGACGCAAAGAACATGATGTGCGCCGCCGACCCTCGTCACGGCCGCTATTTAACTGCCGCGTGTATGTTCCGCGGACGTATGAGCACGAAGGAGGTTGATGAGCAGATGCTGAACGTGCAGAACAAGAACTCGTCGTACTTCGTCGAGTGGATCCCTAACAACATCAAGGCTAGCGTGTGTGACATCCCGCCCAAGGGGCTGAAGATGAGCACTACGTTCATCGGTAACTCGACCGCTATCCAGGAGATGTTCAAGCGTGTGTCTGAGCAGTTTACGGCTATGTTCCGTCGTAAGGCTTTCTTGCACTGGTACACGGGCGAGGGTATGGACGAGATGGAGTTCACGGAGGCCGAGTCCAACATGAATGATCTTGTGT
Phytophthora_ramorum_NA1b     CGACGTCGTCCGCAAGGAGGCCGAGAGCTGTGACTGCCTGCAGGGGTTCCAGATCACGCACTCTCTTGGTGGCGGTACCGGTTCTGGTATGGGCACGCTTCTGATCTCCAAGATCCGTGAGGAGTACCCGGACCGTATCATGTGCACGTACTCGGTGTGCCCGTCGCCCAAGGTGTCGGACACGGTCGTGGAGCCCTACAACGCCACGCTGTCGGTGCACCAGCTTGTCGAGAACGCCGACGAGGTCATGTGCCTGGATAACGAGGCGCTGTACGACATTTGCTTCCGCACGCTCAAGCTCACCACCCCCACCTACGGTGACCTGAACCACCTGGTGTGCGCCGCTATGTCCGGCATCACCACGTGCCTGCGTTTCCCGGGTCAGCTGAACTCGGACCTGCGGAAGCTGGCGGTGAACTTGATTCCGTTCCCGCGTCTTCACTTCTTCATGATTGGTTTCGCCCCGCTGACCTCGCGTGGCTCGCAGCAGTACCGTGCCCTGACGGTGCCCGAGCTGACCCAGCAGCAGTTCGACGCAAAGAACATGATGTGCGCCGCCGACCCTCGTCACGGCCGCTATTTAACTGCCGCGTGTATGTTCCGCGGACGTATGAGCACGAAGGAGGTTGATGAGCAGATGCTGAACGTGCAGAACAAGAACTCGTCGTACTTCGTCGAGTGGATCCCTAACAACATCAAGGCTAGCGTGTGTGACATCCCGCCCAAGGGCCTGAAGATGAGCACTACGTTCATCGGTAACTCGACCGCTATCCAGGAGATGTTCAAGCGTGTGTCTGAGCAGTTTACGGCTATGTTCCGTCGTAAGGCTTTCTTGCACTGGTACACGGGCGAGGGTATGGACGAGATGGAGTTCACGGAGGCCGAGTCCAACATGAACGATCTTGTGT
Phytophthora_ramorum_NA2a     CGACGTCGTCCGCAAGGAGGCCGAGAGCTGTGACTGCCTGCAGGGGTTCCAGATCACGCACTCGCTTGGTGGCGGTACCGGTTCTGGTATGGGCACGCTTCTGATCTCCAAGATCCGTGAGGAGTACCCGGACCGTATCATGTGCACGTACTCGGTGTGCCCGTCGCCCAAGGTGTCGGACACGGTCGTGGAGCCCTACAACGCCACGCTGTCGGTGCACCAGCTTGTCGAGAACGCCGACGAGGTCATGTGCCTGGATAACGAGGCGCTGTACGACATTTGCTTCCGCACGCTCAAGCTCACCACCCCCACCTACGGTGACCTGAACCACCTGGTGTGCGCCGCTATGTCCGGCATCACCACGTGCCTGCGTTTCCCGGGTCAGCTGAACTCGGACCTGCGGAAGCTGGCGGTGAACTTGATTCCGTTCCCGCGTCTTCACTTCTTCATGATTGGTTTCGCCCCGCTGACCTCGCGTGGCTCGCAGCAGTACCGTGCCCTGACGGTGCCCGAGCTGACCCAGCAGCAGTTCGACGCAAAGAACATGATGTGCGCCGCCGACCCTCGTCACGGCCGCTATTTAACTGCCGCGTGTATGTTCCGCGGACGTATGAGCACGAAGGAGGTTGATGAGCAGATGCTGAACGTGCAGAACAAGAACTCGTCGTACTTCGTCGAGTGGATCCCTAACAACATCAAGGCTAGCGTGTGTGACATCCCGCCCAAGGGGCTGAAGATGAGCACTACGTTCATCGGTAACTCGACCGCTATCCAGGAGATGTTCAAGCGTGTGTCTGAGCAGTTTACGGCTATGTTCCGTCGTAAGGCTTTCTTGCACTGGTACACGGGCGAGGGTATGGACGAGATGGAGTTCACGGAGGCCGAGTCCAACATGAACGATCTTGTGT
Phytophthora_ramorum_NA2b     CGACGTCGTCCGCAAGGAGGCCGAGAGCTGTGACTGCCTGCAGGGGTTCCAGATCACGCACTCTCTTGGTGGCGGTACCGGTTCTGGTATGGGCACGCTTCTGATCTCCAAGATCCGTGAGGAGTACCCGGACCGTATCATGTGCACGTACTCGGTGTGCCCGTCGCCCAAGGTGTCGGACACGGTCGTGGAGCCCTACAACGCCACGCTGTCGGTGCACCAGCTTGTCGAGAACGCCGACGAGGTCATGTGCCTGGATAACGAGGCGCTGTACGACATTTGCTTCCGCACGCTCAAGCTCACCACCCCCACCTACGGTGACCTGAACCACCTGGTGTGCGCCGCTATGTCCGGCATCACCACGTGCCTGCGTTTCCCGGGTCAGCTGAACTCGGACCTGCGGAAGCTGGCGGTGAACTTGATTCCGTTCCCGCGTCTTCACTTCTTCATGATTGGTTTCGCCCCGCTGACCTCGCGTGGCTCGCAGCAGTACCGTGCCCTGACGGTGCCCGAGCTGACCCAGCAGCAGTTCGACGCAAAGAACATGATGTGCGCCGCCGACCCTCGTCACGGCCGCTATTTAACTGCCGCGTGTATGTTCCGCGGACGTATGAGCACGAAGGAGGTTGATGAGCAGATGCTGAACGTGCAGAACAAGAACTCGTCGTACTTCGTCGAGTGGATCCCTAACAACATCAAGGCTAGCGTGTGTGACATCCCGCCCAAGGGCCTGAAGATGAGCACTACGTTCATCGGTAACTCGACCGCTATCCAGGAGATGTTCAAGCGTGTGTCTGAGCAGTTTACGGCTATGTTCCGTCGTAAGGCTTTCTTGCACTGGTACACGGGCGAGGGTATGGACGAGATGGAGTTCACGGAGGCCGAGTCCAACATGAACGATCTTGTGT
;
END;

[ The following blocks are output data for analysis step 8870 ]
BEGIN TREES;
      TITLE Btub;
      LINK TAXA = TaxaForAnalysisStep8870;
      TREE Fig._3_Btub = [&R] (((((Phytophthora_ramorum_EU2:0.0011239,Phytophthora_ramorum_EU1b:0.0)0.1560:6.77E-5,(Phytophthora_ramorum_NA2b:0.0,Phytophthora_ramorum_NA1b:0.0)0.7160:0.00112279)0.5050:0.00112279,Phytophthora_ramorum_NA2a:0.0)0.5350:0.00112004,(Phytophthora_ramorum_EU1a:0.00112004,Phytophthora_ramorum_NA1a:0.0):0.0)0.7920:0.00660989,Phytophthora_lateralis:0.0151436,Phytophthora_hibernalis:0.03789781);
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr57177]


END;