#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 November 10, 2024; 21:43 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 2493 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep2493;
        DIMENSIONS NTAX=8;
        TAXLABELS
            Penicillium_brocae_31472
            Penicillium_charlesii_778
            Penicillium_chermesinum_2048
            Penicillium_coffeae_35366
            Penicillium_felllutanum_746
            Penicillium_indicum_3387
            Penicillium_phoeniceum_2070
            Penicillium_thiersii_28162
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M1397]

	TITLE calmodulin;
	LINK TAXA = TaxaForAnalysisStep2493;
	DIMENSIONS NCHAR=743;
	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_31472         GAGGCATTCTCCCTGTTTGTGAGTACCATTTACTACT-GGCTAGAAAAATAAAACGTTGCCTAAAACCAATACTAATGGATACTTTTCCCGGTAATAGGACAAGGATGGCGATGGTGAGTGCGACCGTCTTCGATACCGATGATTTTAGATGCGATCACGCCTGATTTATCGATTGAACAAATA---ACTGAGACGAATAAACTCGACAGGCCAGATTACCACCAAGGAGCTGGGCACTGTCATGCGCTCCCTCGGCCAGAACCCCTCCGAGTCTGAGTTGCAGGACATGATTAACGAGGTTGACGCTGATAACAACGGAACCATTGACTTCCCTGGTACGACCGTCCTTCCC-------------TTCGAACG------ATTCAAGCTCC--AGACCCATATTAACATGCGACACAGAGTTCCTTACCATGATGGCACGTAAGATGAAGGACACCGACTCCGAGGAGGAGATTCGCGAGGCTTTCAAGGTCTTTGACCGCGACAACAACGGATTTATCTCTGCCGCCGAGCTGCGCCATGTGATGACCTCAATTGGTGAGAAGCTGACTGACGACGAGGTGGACGAGATGATCCGTGAGGCGGACCAGGATGGTGATGGTCGCATTGACTGTATGTTCCCTCGGAAACCCCGC-CCTCGAACTGCAACAGCGGGCCT----TATCTACAC--GATTCACTAGAACAC---ACAAGCTGACCTATC--ACAGACAACGAGTTC
Penicillium_charlesii_778        GAGGCGTTCTCCCTCTTCGTAAGTTG--TCTGATCTTTGATTGCGGATTTTGTTTGGCCTAGGGAAACGCAGCTAACC-GCGTTATTCTC---AACAGGACAAGGATGGCGATGGTGAGTGC--------------CCGATGACACCAGACAT--TAAAGCCC--TCCAGCAATTGGAGTCATCTTGACTGAGACGAAATGATCA-TTAGGACAAATCACCACCAAGGAGCTTGGCACTGTCATGCGCTCGCTTGGCCAGAACCCCTCCGAGTCTGAGCTGCAGGACATGATCAACGAAGTCGACGCCGACAACAACGGCACCATTGATTTCCCCGGTATAAAATTGCTGCACCC--CCTTCCCTCTCTGGCC--CTTCTCGGTTGAC-CC--GGACTGTTACTGATCTTCG-ACTAGAATTCCTTACCATGATGGCCCGCAAGATGAAGGATACCGACTCAGAGGAGGAGATTCGCGAGGCATTCAAGGTGTTCGATCGCGACAACAACGGTTTCATCTCCGCCGCTGAGCTGCGTCACGTCATGACCTCCATCGGCGAGAAGCTGACCGACGACGAGGTGGACGAGATGATCCGTGAAGCCGACCAGGACGGGGATGGCCGTATCGACTGTACGTTCCAGCAGGCCGGGAAAGCCCCTCGGTTTCTCCACTGCTCTCGTCAACCCCCCCCCTCTTCACCACATTCCCTGCTAACATTGAGTTTCTGATAGACAACGAGTTC
Penicillium_chermesinum_2048     GAGGCGTTCTCCCTCTTCGTAAGTGC--TCCGATCTT-GATCGCGGGTTTTGCTTG-CCTTGCAACACTTAGCTAACCAGTAATGCCTTGG--AATAGGACAAGGATGGCGATGGTGAGTGCGA---TCTGCGCC-CGGGCGACACTAGGCACTCTCGGTCAT----GAGCAATCGAGGAAATTTTTACTGAGACGAATTGATGA-ATAGGACAAATCACCACCAAGGAGCTGGGCACTGTCATGCGCTCTCTCGGCCAGAACCCCTCCGAGTCTGAGCTGCAGGACATGATCAATGAGGTTGACGCTGATAACAACGGCACCATCGATTTTCCCGGTACGAGATACCTGCGATTT--------TCTAGGACC--C--CACTGCTTCCACCTAGATCGTTTACTGACGTTCA--ATAGAGTTCCTTACCATGATGGCCCGTAAGATGAAGGATACCGACTCAGAGGAGGAGATTCGGGAGGCATTCAAGGTGTTCGACCGTGACAACAACGGCTTCATCTCTGCTGCTGAGCTGCGCCATGTCATGACCTCCATCGGTGAGAAGCTAACCGACGATGAGGTTGATGAGATGATCCGCGAAGCGGACCAGGATGGCGATGGCCGTATCGACTGTAAGTCTCAATA-AACGGGAAAGCTCC--------TCAAGCTTTCTCGCTCATTCCTTCGACCGCCCTCCGGTCCAATGCTAACCACGCAATTCGTGTAGACAACGAGTTC
Penicillium_coffeae_35366        GAGGCGTTCTCCCTCTTTGTAAGTAC--AGCGAGGAT-GATA---AATCTCG---------GGAATACCCTGCTAACC-TGAATTACCTG---TACAGGACAAGGATGGCGATGGTAAGCCTAA---TCTCCGC--CCGACAACACTGGACAC-AACAAGCCT---TT-GCAATTGGAATATCCCCGACTAAGACGAATTGAATA-ATAGGCCAGATCACCACCAAGGAGCTTGGTACCGTCATGCGCTCCCTCGGCCAGAACCCCTCCGAGTCTGAGCTGCAGGACATGATCAACGAGGTTGACGCCGACAACAACGGCACCATTGATTTCCCTGGTATGTGATTCCTGCGCTGTTCACCGGAACTCCATGCGACTTTTGTTCTTCGTCC--GGACCTGTGCTTACAA-CATAACAGAGTTCCTTACCATGATGGCCCGCAAGATGAAGGATACCGACTCAGAGGAGGAGATTCGTGAGGCATTCAAGGTGTTCGACCGTGACAACAACGGCTTCATCTCCGCCGCCGAGCTGCGCCACGTCATGACTTCCATTGGTGAGAAGCTGACCGACGACGAAGTGGACGAGATGATCCGCGAGGCGGACCAGGATGGCGACGGCCGTATTGACTGTATGTCACTCCA-----------CCCCAA----TCCCGGGAGGCCT----ATTTCCCAC--CCTTCATCGCTTGT--TGCTAACCGTCCGGAAC----AGACAACGAGTTC
Penicillium_felllutanum_746      GAGGCGTTCTCCCTCTTCGTAAGTTG--TCTGATCTT-GATTGCGAATTTTGTTTGGCCTAGGGAAACGCAGCTAACC-ATGTTATTTTC---AACAGGACAAGGATGGCGATGGTGAGTGC--------------CCGACGACACCAGACAT-AAAAGTCCC---CCAGCAATTGGAATCATTTTTACTGAGACGAAATGGTGA-TTAGGACAAATCACCACCAAGGAGCTTGGCACTGTCATGCGCTCGCTTGGCCAGAACCCCTCCGAGTCTGAGCTGCAGGACATGATCAACGAAGTCGACGCCGATAACAACGGCACCATTGATTTCCCCGGTACAAAATTGCTGCAC----CACCCCCTCTCCGGCC--CTTCTCAGCTGAC-CC--GGACTGTTACTGATTT-CG-ACTAGAATTCCTTACCATGATGGCCCGCAAGATGAAGGATACCGACTCAGAGGAGGAGATTCGCGAGGCATTCAAGGTGTTCGACCGCGACAACAACGGTTTCATCTCCGCCGCTGAGCTGCGTCATGTCATGACCTCCATCGGCGAGAAGCTGACCGACGACGAGGTGGACGAGATGATCCGTGAAGCTGACCAGGACGGTGATGGCCGTATCGACTGTACGTTCCAGCAGATCGGGAGAGCCCCTCGGTTTCCCCACTGCTCCCGTCAATCCCCCC--TCTTCACCACATTCCATGCTAACATTAGGTTTCTGATAGACAACGAGTTC
Penicillium_indicum_3387         GAGGCGTTCTCCCTCTTTGTAAGTGC--TCCGATCTT-GATTGCGTGTCTTGCTTGACTTGGAACGCTTTAGCTAACAAATAATGCCCTG--TAATAGGACAAGGATGGCGATGGTGAGTGCGA---TCTGCGCC-CGGGCGACACTAGGCAC--TCTTGGCCA--TGAGAAATTGAAGAAATTTTTACTGAGACGGATCAATGA-ACAGGACAAATCACCACCAAGGAGCTCGGCACTGTCATGCGCTCTCTCGGCCAGAACCCCTCCGAGTCTGAGCTGCAGGACATGATCAATGAGGTTGACGCCGATAACAACGGCACTATCGATTTCCCCGGTACGAGACATCTGCGAT----------TTTCTATACCCTCACTAAATTCACTCA--GACCTTTTACTGACGTCCA--ATAGAGTTCCTTACCATGATGGCTCGTAAGATGAAGGATACCGACTCAGAGGAGGAGATTCGGGAGGCATTCAAGGTGTTCGACCGTGACAACAACGGTTTCATCTCCGCCGCTGAGCTGCGCCATGTCATGACCTCCATCGGTGAGAAGCTCACCGACGATGAGGTTGATGAGATGATCCGCGAAGCGGACCAGGATGGCGACGGCCGTATCGACTGTAAGTCTCAATT-AACGGGAAAGCCCC--------TCAACTTCCCTACTTATTCCTTCGAACCTCCCTTTGATTAA-TGCTAACCATTCTATTCACGTAGACAACGAGTTC
Penicillium_phoeniceum_2070      GAGGCCTTCTCCCTTTTCGTAAGTAC--ATCGATGAT----G----ATATAGCTCC-CGCGAGGATTCCCTACTAACC-AGAAATACCTG---CACAGGACAAGGATGGCGATGGTAAGCCTAA---TATCCGC--CCGACAACATTGGACAG-ATCAAGTCT----CTGCAATTGAGAGATCCCCGGCTAAGACGAATTGAACA-ATAGGACAAATCACCACCAAGGAGCTTGGTACCGTCATGCGCTCCCTCGGCCAGAACCCCTCCGAGTCTGAGCTTCAGGACATGATCAACGAGGTTGACGCCGACAACAACGGCACCATCGATTTCCCTGGTATGTCATACCTGCGATTCCCATCGGAGCTACACGCGAGTTTCGTGCTTCGCTA--GGACCTGCGCTGACAC-CTCCACAGAGTTCCTTACCATGATGGCCCGCAAGATGAAGGATACCGACTCAGAGGAGGAGATTCGTGAGGCATTCAAGGTGTTCGACCGCGACAACAACGGTTTCATCTCCGCCGCCGAGCTGCGCCACGTCATGACCTCCATTGGTGAGAAGCTTACCGACGACGAAGTGGATGAGATGATCCGCGAGGCGGACCAGGATGGCGACGGCCGTATTGACTGTATGTCCCGAGA-----------------A---TCTCGGGAGGCCC---CATTTCCCGC--CCCTCGTCGCTTGGC--GCTAACCGATCGAAAT----AGACAACGAGTTC
Penicillium_thiersii_28162       GAGGCCTTCTCCTTGTTTGTGAGTAACCTGATCTATT-GATTC--AAGGTTATTGG----CTTGGTTTAGTACTAATGGATACTTTCTCCGGCCATAGGACAAGGATGGCGATGGTGAGTGCGA----C--CGTTTACGATGACTTCAAGCTTGATTGTGCCA----CGGCCATTCAGCGACCAATAACTAAGAC-AAGTGATCA-ATAGGACAAATCACCACCAAGGAGCTGGGTACTGTCATGCGCTCCCTCGGCCAGAACCCCTCTGAGTCTGAGCTGCAGGACATGATTAATGAGGTCGACGCTGACAACAACGGCACCATTGACTTCCCTGGTATGACTTCTCCTCAAA----ACTCGCAATCACGCCG--GGGTATTCTACC-CG--AGACTCATAATAACTTGCG--ACAGAATTCCTCACCATGATGGCCCGTAAGATGAAAGACACCGACTCCGAGGAGGAGATTCGTGAGGCATTCAAGGTGTTCGACCGCGATAACAACGGTTTTATCTCCGCGGCCGAACTGCGCCATGTCATGACTTCGATCGGCGAGAAGCTGACCGATGATGAGGTGGATGAGATGATCCGCGAGGCGGACCAGGATGGTGATGGCCGGATCGACTGTATGCTTCCCTT-----------TCCCTTTCGGGACCAAGCATTTG----ACTTTCCAT----GTCATCGGAACA--TGTCGCGCTAACCTATC--ACAGACAACGAGTTC
;
END;

BEGIN CODONS;
CODONPOSSET * CodonPositions (CHARACTERS = calmodulin) = 
		N: 1-743;
CODONPOSSET  CodonPositions (CHARACTERS = calmodulin) = 
		N: 1-743;
END;
[ The following blocks are output data for analysis step 2493 ]
BEGIN TREES;
      TITLE Tb7268;
      LINK TAXA = TaxaForAnalysisStep2493;
      TREE Fig._1l = [&R] (Penicillium_thiersii_28162,((((Penicillium_charlesii_778,Penicillium_felllutanum_746),(Penicillium_chermesinum_2048,Penicillium_indicum_3387)),(Penicillium_phoeniceum_2070,Penicillium_coffeae_35366)),Penicillium_brocae_31472));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr645]


END;