#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 21, 2025; 4:45 GMT

TreeBASE (cc) 1994-2008

Study reference:
Peterson S., Vega F., Posada F., & Nagai C. 2005. Penicillium coffeae a new endophytic
species isolated from a coffee plant and its phylogenetic relationship to
P. fellutanum, P. thiersii and P. brocae based on parsimony analysis of multilocus
DNA sequences. Mycologia, null.

TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S1335]

[ The following blocks are input data for analysis step 2492 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep2492;
        DIMENSIONS NTAX=8;
        TAXLABELS
            Penicillium_brocae
            Penicillium_charlesii
            Penicillium_chermesinum
            Penicillium_coffeae
            Penicillium_fellutanum
            Penicillium_indicum
            Penicillium_phoeniceum
            Penicillium_thiersii
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M1396]

	TITLE 'ef-1alpha';
	LINK TAXA = TaxaForAnalysisStep2492;
	DIMENSIONS NCHAR=742;
	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  ]
[                                    .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .  ]
Penicillium_brocae          AGCACATCAACATCGTCGTTATCGGCCACGTCGATTCCG---------------------------------------------------------GCAAGTCCACCACCACCGGTAAGCTCCAGCCTCCCCTCACTT-CAAACCCCTCCCTCCTATGCCATCGAACAACAAGACTGATTCATCCATTACAGGTCACTTGATCTACAAGTGTGGTGGTATCGACTCTCGTACCATCGAGAAGTTCGAGAAGGAGGCCGCTGAGCTCGGTAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGATATTGCCCTCTGGAAGTTCCAGACCTCCAAGTATGAGGTTACCGTCATTGATGCCCCCGGTCACCGTGACTTCATCAAGAACATGATCACTGGTACCTCCCAGGCTGACTGCGCCATTCTCATCATTGCCTCCGGTACTGGTGAGTTCGAGGCTGGTATCTCCAAGGATGGCCAGACCCGTGAGCACGCTCTGCTTGCCTTCACCCTCGGTGTCCGCCAGCTCATCGTCGCCCTGAACAAGATGGACACTTGCAAGTGGGCTGAGGAGCGTTACAACGAGATTGTCAAGGAGACCTCCAACTTCATCAAGAAGGTCGGCTACAACCCCAAGGGTGTCCCCTTCGTCCCCATCTCCGGTTTCAACGGTGACAACATGCTGGAGGCCTCCACCAACTGCCCCTG
Penicillium_charlesii       AGCACATCAACATCGTCGTTATCGGCCACGTCGATTCCG---------------------------------------------------------GCAAGTCCACCACCACCG------------------------------------------------------------------------------GTCACTTGATCTACAAGTGTGGAGGTATCGACTCTCGTACCATCGAGAAGTTCGAGAAGGAAGCCGCTGAACTCGGTAAGGGTTCCTTCAAGTATGCCTGGGTTCTCGACAAACTCAAGGCTGAGCGTGAGCGTGGTATCACCATCGACATTGCTCTCTGGAAGTTCCAGACCAGCAAGTTCGAGGTTACCGTCATTGACGCCCCCGGTCACCGTGACTTCATCAAGAACATGATCACTGGTACCTCCCAGGCTGACTGCGCCATTCTCATCATTGCCTCCGGTACCGGTGAGTTCGAGGCTGGTATCTCCAAGGATGGCCAGACCCGTGAGCACGCTCTGCTTGCTTTCACCCTCGGTGTGCGTCAGCTCATCGTTGCCCTGAACAAGATGGACACTTGCAAGTGGGCTGAGGACCGTTACAACGAAATTGTTAAGGAGACCTCCAACTTCATCAAGAAGGTCGGCTACAACCCCAAGTCCGTTCCCTTCGTCCCCATCTCCGGTTTCAACGGTGACAACATGCTTGAGCCCTCCACCAACTGCCCCTG
Penicillium_chermesinum     AGCACATCAACATCGTCGTTATCGGCCACGTCGATTCCG---------------------------------------------------------GCAAGTCCACCACCACTG------------------------------------------------------------------------------GTCACCTGATCTACAAGTGTGGTGGTATCGACTCTCGTACCATCGAGAAGTTCGAGAAGGAAGCCGCTGAGCTCGGTAAGGGTTCCTTCAAGTATGCCTGGGTTCTGGACAAATTGAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCCCTCTGGAAGTTCCAGACCAGCAAGTTCGAGGTTACCGTCATTGATGCCCCCGGTCACCGTGACTTCATCAAGAACATGATCACTGGTACCTCCCAGGCCGACTGCGCTATCCTCATCATCGCTTCCGGCACTGGTGAGTTCGAGGCTGGTATCTCCAAGGATGGCCAGACCCGTGAGCACGCTCTGCTTGCTTTCACCCTCGGTGTGCGTCAGCTCATCGTCGCTCTTAACAAGATGGACACCTGCAAGTGGTCCGAGGAGCGTTACAACGAGATTGTCAAGGAGACCTCCAACTTCATCAAGAAGGTTGGCTACAACCCCAAGAGTGTCCCCTTCGTCCCCATCTCCGGTTTCAACGGTGACAACATGCTTGAGCCCTCCCCCAACTGCCCCTG
Penicillium_coffeae         AGCACATCAACATCGTCGTTATCGGCCACGTCGATTCCGGTAAGCCATCCTCCCTCCATCACATATCATCATAACAATGACTGATCCCTCCCTCAGGCAAGTCCACCACCACTG------------------------------------------------------------------------------GTCACTTGATCTACAAGTGCGGTGGTATCGACTCTCGTACCATCGAGAAGTTCGAGAAGGAAGCCGCTGAGCTCGGCAAGGGTTCCTTCAAGTATGCCTGGGTTCTCGACAAATTGAAGGCTGAGCGTGAGCGTGGTATCACCATCGATATCGCTCTCTGGAAGTTCCAGACCTCTAAGTTCGAGGTTACCGTCATTGACGCCCCCGGTCACCGTGACTTCATCAAGAACATGATCACTGGTACCTCCCAGGCTGACTGTGCCATTCTCATCATCGCCTCCGGCACTGGTGAGTTCGAGGCTGGTATCTCCAAGGATGGCCAGACCCGTGAGCACGCTCTGCTTGCTTTCACCCTCGGTGTGCGTCAGCTCATCGTTGCCCTGAACAAGATGGACACTTGCAAGTGGGCCGAGGACCGTTACAACGAGATTGTCAAGGAGACCTCCAACTTCATCAAGAAGGTCGGCTACAACCCCAAGTCCGTTCCCTTCGTCCCCATCTCCGGTTTCAACGGTGACAACATGCTTGAGCCCTCCACCAACTGCCCCTG
Penicillium_fellutanum      AGCACATCAACATCGTCGTTATCGGCCACGTCGATTCCG---------------------------------------------------------GCAAGTCCACCACCACCG------------------------------------------------------------------------------GTCACTTGATCTACAAGTGTGGAGGTATCGACTCTCGTACCATCGAGAAGTTCGAGAAGGAAGCCGCTGAACTCGGCAAGGGTTCCTTCAAGTATGCCTGGGTTCTCGACAAACTCAAGGCTGAGCGTGAGCGTGGTATCACCATCGACATTGCTCTCTGGAAGTTCCAGACCAGCAAGTTCGAGGTTACCGTCATTGACGCCCCCGGTCACCGTGACTTCATCAAGAACATGATCACTGGTACCTCCCAGGCTGACTGTGCCATTCTCATCATTGCCTCCGGTACCGGTGAGTTCGAGGCTGGTATCTCCAAGGATGGCCAGACCCGTGAGCACGCTCTGCTTGCTTTCACCCTCGGTGTGCGTCAGCTCATCGTTGCCCTGAACAAGATGGACACTTGCAAGTGGGCCGAGGACCGTTACAACGAAATTGTCAAGGAGACCTCCAACTTCATCAAGAAGGTCGGCTACAACCCCAAGTCCGTTCCCTTCGTCCCCATCTCCGGTTTCAACGGTGACAACATGCTTGAGCCCTCCCCCAACTGCCCCTG
Penicillium_indicum         AGCACATCAACATCGTCGTTATCGGCCACGTCGATTCCG---------------------------------------------------------GCAAGTCCACCACCACTG------------------------------------------------------------------------------GTCACCTGATCTACAAGTGTGGTGGTATCGACTCTCGTACCATCGAGAAGTTCGAGAAGGAAGCCGCTGAGCTCGGTAAGGGTTCCTTCAAGTATGCCTGGGTTCTCGACAAATTGAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCTCTCTGGAAGTTCCAGACCAGCAAGTTCGAGGTTACCGTCATTGACGCCCCTGGTCACCGTGACTTCATCAAGAACATGATCACTGGTACCTCCCAGGCCGACTGTGCCATTCTCATCATCGCCTCCGGCACTGGTGAGTTCGAGGCTGGTATCTCCAAGGATGGCCAGACCCGTGAGCACGCTCTGCTTGCTTTCACCCTCGGTGTGCGTCAGCTCATCGTCGCTCTTAACAAGATGGACACCTGCAAGTGGTCCGAGGAGCGTTACAACGAGATTGTCAAGGAGACCTCCAACTTCATCAAGAAGGTTGGCTACAACCCCAAGAGCGTCCCCTTCGTCCCCATCTCCGGTTTCAACGGTGACAACATGCTCGAGCCCTCCCCCAACTGCCCCTG
Penicillium_phoeniceum      AGCACATCAACATCGTCGTTATCGGCCACGTCGATTCCGGTAAGCCATCCTTCTTCGATACCATCCATCACAACAGTGACTGATCCATCCCCACAGGCAAGTCCACCACCACCG------------------------------------------------------------------------------GTCACTTGATCTACAAGTGTGGTGGTATCGACTCTCGTACCATCGAGAAGTTCGAGAAGGAAGCCGCCGAGCTCGGCAAGGGTTCCTTCAAGTATGCCTGGGTTCTCGACAAATTGAAGGCTGAGCGTGAGCGTGGTATCACCATCGATATCGCTCTCTGGAAGTTCCAGACCGCTAAGTTCGAGGTTACCGTCATTGACGCCCCTGGTCACCGTGACTTCATCAAGAACATGATCACTGGTACCTCCCAGGCTGACTGTGCCATTCTCATCATCGCCTCCGGCACTGGTGAGTTCGAGGCTGGTATCTCCAAGGATGGCCAGACCCGTGAGCACGCTCTGCTTGCTTTCACCCTCGGTGTGCGTCAGCTCATCGTTGCCCTGAACAAGATGGACACCTGCAAGTGGGCCGAGGAGCGTTACAACGAGATTGTCAAGGAGACCTCCAACTTCATCAAGAAGGTCGGCTACAACCCCAAGACCGTCCCCTTCGTCCCCATCTCCGGTTTCAACGGTGACAACATGCTTGAGCCCTCCCCCAACTGCCCCTG
Penicillium_thiersii        AGCACATCAACATCGTCGTTATCGGCCACGTCGATTCCG---------------------------------------------------------GCAAGTCCACCACCACCGGTAAGCTTCAACCCCTCCTCCCTT-GTCCACAGTCCTTCC-----CATCAAACAACATT-CTAATCCATCAAT-ACAGGTCACTTGATCTACAAGTGCGGTGGTATCGACTCTCGTACCATCGAGAAGTTCGAGAAGGAGGCTGCTGAGCTCGGTAAGGGTTCCTTCAAGTACGCCTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGATATCGCTCTCTGGAAGTTCCAGACCGCCAAGTATGAGGTCACCGTCATTGATGCCCCCGGTCACCGTGATTTCATCAAGAACATGATCACTGGTACCTCCCAGGCCGATTGCGCTATTCTCATCATCGCCTCCGGCACTGGTGAGTTCGAGGCTGGTATCTCCAAGGATGGCCAGACCCGTGAGCACGCTCTGCTTGCCTTCACCCTCGGTGTCCGCCAGCTCATCGTTGCCCTGAACAAGATGGACACCTGCAAGTGGTCCGAGGACCGTTACAACGAGATCGTCAAGGAGACCTCCAACTTCATCAAGAAGGTTGGCTACAACCCCAAGAGCGTTCCCTTCGTTCCCATCTCCGGCTTCAACGGTGACAACATGCTTGAGCCCTCCCCCAACTGCCCCTG
;
END;

BEGIN CODONS;
CODONPOSSET * CodonPositions (CHARACTERS = 'ef-1alpha') = 
		N: 1-742;
CODONPOSSET  CodonPositions (CHARACTERS = 'ef-1alpha') = 
		N: 1-742;
END;
[ The following blocks are output data for analysis step 2492 ]
BEGIN TREES;
      TITLE Tb7267;
      LINK TAXA = TaxaForAnalysisStep2492;
      TREE Fig._1r = [&R] (Penicillium_thiersii,(((Penicillium_chermesinum,Penicillium_indicum),(Penicillium_phoeniceum,(Penicillium_coffeae,(Penicillium_fellutanum,Penicillium_charlesii)))),Penicillium_brocae));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr2095]


END;