#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 12, 2024; 21:18 GMT

TreeBASE (cc) 1994-2008

Study reference:
Gu W., Li M., Xu Y., Wang T., Ko J., & Zhou T. 2014. The impact of RNA structure
on coding sequence evolution in both bacteria and eukaryotes. BMC Evolutionary Biology,
.

TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S15642]

BEGIN TAXA;
        TITLE  Taxa;
        DIMENSIONS NTAX=10;
        TAXLABELS
            Escherichia_coli
            Klebsiella_pneumoniae
            Photorhabdus_luminescens
            Salmonella_enterica
            Salmonella_typhimurium
            Shigella_boydii
            Shigella_dysenteriae
            Shigella_flexneri
            Shigella_sonnei
            Sodalis_glossinidius
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M21765]

	TITLE ecoli_data_Matrix;
	LINK TAXA = Taxa;
	DIMENSIONS NCHAR=930;
	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       910       920       930]
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Escherichia_coli             ATGGTTAAAGTTTATGCCCCGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGACACCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAACTGGGTAAGCAAATTCCAGTGGCGATGACCCTGGAAAAGAATATGCCGATCGGTTCGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGCGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTCGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGCAAGTGCCAGGGTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAAGTCTCGACGGCAGAAGCCAGGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGGCGACATCTGGCAGGCTTCATTCACGCCTGCTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAAAGATGTTATCGCTGAACCCTACCGTGAACGGTTACTGCCAGGCTTCCGGCAGGCGCGGCAGGCGGTCGCGGAAATCGGCGCGGTAGCGAGCGGTATCTCCGGCTCCGGCCCGACCTTGTTCGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAAC
Klebsiella_pneumoniae        ATGGTCAAAGTATATGCCCCGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGTTGGGCGCGGCGGTCACGCCGGTGGATGGCACGCTGCTGGGCGATAACGTCACTGTTGAAGCGGCGGAGCAATTCAGTCTGCACAATCTGGGACGCTTCGCCAGCAAACTGCCGACGGCGCCTCAGGAAAACATTGTTTATCAGTGCTGGGAAAGCTTTTGCCAGGAGATCGGTAAGACGGTACCGGTGACGATGACCCTGGAAAAAAACATGCCGATCGGCTCCGGGCTCGGCTCCAGCGCCTGCTCGGTGGTCGCCGCGCTGGTGGCCATGAACGAGTTCTGCGGTAAGCCGCTCAACGAGACGCGGATGCTGGCGCTGATGGGGGAGATGGAAGGGCGTATCTCCGGCAGCATTCACTACGATAACGTGGCGCCGTGCTATCTTGGCGGCATGCAGTTGATGATCGAAGAGAACGGGATTATCAGCCAGCAGGTGCCGGGGTTTGATGAGTGGCTGTGGGTGTTGGCCTATCCGGGGATTAAAGTATCCACCGCCGAAGCGCGGGCGATTCTGCCGGCACAATACCGCCGCCAGGATTGTATCGCCCATGGTCGCCACCTCGCGGGCTTTATTCATGCCTGCTACACCCGCCAGCCGCAGCTGGCGGCAAAATTGATGAAAGATGTCATTGCCGAACCGTACCGTACCAAACTGTTGCCGGGCTTTAGCGAAGCGCGCCAGGCGACAATGGAGATCGGTGCGCAGGCTTGCGGCATCTCCGGCTCTGGCCCGACGCTGTTTGCGTTGTGTGATAAACCGGACACCGCACAGCGCGTCGCCGACTGGCTTGGCGCGCACTATCTGCAGAATCAGGAAGGCTTTGTTCATATTTGCCGGCTGGACACGGCGGGCGCACGCGTAGTGGGA---
Photorhabdus_luminescens     GTGATTAAAGTCTATGCGCCTGCATCTATTGGTAATGTCAGTGTTGGGTTTGATGTACTGGGAGCGGCGGTCTCTCCAGTTAATGGTGCTTTATTAGGTGACTGCGTTACTGTTCGGGCAGCGAAGAGTTTCAGTTTGCGTAATGAAGGGCAGTTTGTGGGGAAGTTACCTGAGAAGCTGGAGCACAACATTGTTTATCAATGCTGGCAATTATTCTGCCAGCATTTGGGCAAACAATTACCAGTGGAAATGACGCTGGAAAAAAATATGCCAATTGGTTCTGGCCTTGGCTCCAGCGCTTGTTCTGTTGTTGCAGGTTTGATGGCACTGAACGAGTTTGCAGGTCTCCCATTTAATGAAAGCCAATTACTGGCAATGATGGGGGAACTGGAAGGACGTATTTCCGGCAGTATTCACTATGATAATGTCGCTCCATGCTATCTCGGCGGTTTGCAACTGATTATGGAACAAGGAGATATTATCTGTCAGCCAGTACCTTCGTTTGATGAGTGGTTATGGGTGATGGCCTATCCGGGCATCAAAGTTTCTACCGCAGAAGCCAGAGCAATTTTACCTGTAAAATATTCGAAGCAGGATGTTATCGATCATGGACGTTTTCTTGCCGGGTTTATTCATGCCTGTCATACACGGCAACCGGCGCTGGCCGCCAGATTGATGAAAGATGTGGTTGCTGAACCGTATCGTACCCAACTGTTACCGGGTTTTGCCAATGCGCGTGAAACAGCAAAACGGGTAGGGGCATTGGCGTGTGGTATTTCTGGTTCTGGCCCGACATTGTTTTCCATTTGTAATGATATAGCGACCGCAGAGGAAATAGCTGAGTGGCTGCAACAGCATTATGTTCAGAATGATGAAGGTTTTGTACACATTTGCCGTCTGGATCTCGCAGGCGCACGACAAATAGGG---
Salmonella_enterica          ATGGTGAAAGTGTATGCCCCGGCTTCCAGCGCGAACATGAGCGTCGGTTTCGACGTGTTGGGCGCGGCCGTCACACCCGTTGACGGCACGTTGCTGGGCGATGTGGTATCCGTTGAAGCAGCGGATCATTTCCGTCTGCATAACCTGGGGCGATTTGCCGATAAACTGCCGCCGGAGCCGCGTGAAAATATTGTTTATCAGTGCTGGGAACGTTTTTGCCAGGCATTGGGGAAAACCATCCCGGTGGCGATGACGCTGGAAAAAAATATGCCGATTGGTTCCGGGTTAGGGTCCAGCGCCTGTTCCGTCGTCGCCGCGCTGGTCGCGATGAATGAGCACTGCGGCAAACCGTTAAACGACACGCGTCTGTTGGCGCTGATGGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATCCATTACGATAACGTCGCGCCGTGCTTTCTTGGCGGTATGCAGTTGATGATTGAAGAAAACGGCATTATTAGTCAGCAGGTGCCGGGCTTTGATGAGTGGCTATGGGTACTGGCTTATCCGGGCATTAAAGTTTCCACCGCAGAAGCACGGGCCATTTTGCCTGCGCAGTATCGCCGTCAGGATTGCATTGCGCATGGACGGCATCTGGCCGGTTTTATTCACGCCTGTTACTCGCGGCAGCCGCAGCTTGCCGCCGCGCTGATGAAAGATGTTATTGCCGAACCATACCGCGCGCGTTTACTGCCGGGCTTTAGCCAGGCGCGGCAGGCGGTGTCGGAGATCGGCGCGCTGGCGAGCGGGATTTCCGGATCGGGGCCGACGCTGTTTGCGCTATGCGATAAACCGGAGACGGCGCAGCGCGTCGCGGACTGGCTGAGCAAACATTATCTGCAAAATCAGGAAGGCTTCGTTCATATTTGTCGGCTGGATACGGCGGGCGCACGAGTAGTGGGA---
Salmonella_typhimurium       ATGGTGAAAGTGTATGCCCCGGCTTCCAGCGCGAACATGAGCGTCGGTTTCGACGTGTTGGGCGCAGCCGTCACACCCGTTGACGGCACGTTGCTGGGCGATGTGGTATCCGTTGAAGCAGCGGACCATTTCCGTCTGCATAACCTGGGGCGATTTGCCGATAAACTGCCGCCGGAGCCGCGTGAAAATATTGTTTATCAGTGCTGGGAACGTTTTTGCCAGGCATTGGGGAAAACCATCCCGGTGGCGATGACGCTGGAAAAAAATATGCCGATTGGTTCCGGGTTAGGGTCCAGCGCCTGTTCCGTCGTCGCCGCGCTGGTCGCGATGAATGAGCACTGCGGCAAACCGTTAAACGACACGCGTCTGTTGGCGCTGATGGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATCCATTACGATAACGTCGCGCCGTGCTTTCTTGGCGGTATGCAGTTGATGATTGAAGAAAACGGCATTATTAGTCAGCAGGTGCCGGGCTTTGATGAGTGGCTATGGGTACTGGCTTATCCGGGCATTAAAGTTTCTACCGCAGAAGCACGGGCCATTTTGCCTGCGCAGTATCGCCGTCAGGATTGCATTGCGCATGGACGGCATCTGGCCGGTTTTATTCACGCCTGTTACTCGCGGCAGCCGCAGCTTGCCGCCGCGCTGATGAAAGATGTTATTGCCGAACCATACCGCGCGCGTTTACTGCCGGGCTTTAGCCAGGCGCGGCAGGCGGTGTCGGAGATCGGCGCGCTGGCGAGCGGGATTTCCGGGTCGGGGCCGACGCTGTTTGCGCTATGCGATAAACCGGAGACGGCGCAGCGCGTCGCGGACTGGCTGAGCAAACATTATCTGCAAAATCAGGAAGGCTTCGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTAGTGGGA---
Shigella_boydii              ATGGTTAAAGTTTATGCCCCGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGACACCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAGCTTGGCAAGCAAATTCCAGTGGCGATGACTCTGGAAAAGAATATGCCAATCGGTTCGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGTGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGACGAATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTTGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGCAAGTGCCAGGGTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAAGTCTCAACGGCAGAAGCCAGGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGGCGACATCTGGCTGGCTTCATTCACGCCTGCTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAAAGATGTTATCGCTGAACCCTACCGTGAACGGTTACTGCCTGGCTTCCGGCAGGCGCGGCAGGCGGTTGCGGAAATCGGCGCGGTAGCGAGCGGTATCTCCGGCTCCGGCCCGACCTTGTTCGCTCTGTGTGACAAGCCGGATACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAAC
Shigella_dysenteriae         ATGGTTAAAGTTTATGCCCCGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGACACCCGTTGATGGTGCATTGCTCGGAGATGTAGTAACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAGCTGGGCAAGCAAATTCCAGTGGCGATGACTCTGGAAAAGAATATGCCGATCGGTTCGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGCGGCAAGCCGCTTAATGACACCCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGGCGTATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTTGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGCAAGTGCCAGGGTTTGATGAGTGGCTGTGGGTACTGGCGTATCCGGGGATTAAAGTCTCGACGGCAGAAGCCCGGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGGCGACATCTGGCAGGCTTCATTCACGCCTGCTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAAAGATGTTATCGCAGAACCCTACCGTGAACGGTTACTGCCTGGCTTCCGGCAGGCGCGGCAGGCGGTCGCGGAAATCGGCGCGGTAGCGAGCGGTATCTCCGGATCCGGCCCGACCTTGTTCGCTCTGTGTGACAAGCCGGATACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAAC
Shigella_flexneri            ATGGTTAAAGTTTATGCCCCGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGGCACCCGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAGCTTGGCAAGCAAATTCCAGTGGCGATGACTCTGGAAAAGAATATGCCGATCGGTTCGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGCGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGACGTATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTTGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGCAAGTGCCAGGGTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGAATTAAAGTCTCGACGGCAGAAGCCCGGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGGCGACATCTGGCTGGCTTCATTCACGCCTGCTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAAAGATGTTATCGCTGAACCCTACCGTGAACGGTTACTGCCTGGCTTCCGGCAGGCGCGGCAGGCGGTCGCGGAAATCGGCGCGGTAGCGAGCGGTATCTCCGGCTCCGGCCCGACCTTGTTCGCTCTATGTGACAAGCCGGATACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAAC
Shigella_sonnei              ATGGTTAAAGTTTATGCCCCGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGACACCCGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCTGGAGCTGGGCAAGCAAATTCCAGTGGCGATGACTCTGGAAAAGAATATGCCGATCGGCTCGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGCGGCAAGCCACTTAATGACACCCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGACGTATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTTGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGCAAGTGCCAGGGTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGAATTAAAGTCTCGACGGCAGAAGCCCGGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGGCGACATCTGGCTGGCTTCATTCACGCCTGCTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAAAGATGTTATCGCTGAACCCTACCGTGAACGGTTACTGCCTGGCTTCCGGCAGGCGCGGCAGGCGGTCGCGGAAATCGGCGCGGTAGCGAGCGGTATCTCCGGCTCCGGCCCGACCTTGTTCGCTCTATGTGACAAGCCGGATACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAAC
Sodalis_glossinidius         ATGGTTAAAGTGTATGCGCCGGCCTCAATCGGCAACGTCAGCGTGGGATTCGACGTGCTGGGCGCGGCGGTGTCGCCTGTGGACGGGACGCTACTGGGGGATTGCGTCAGCGTATCCCGCGCCGACAGCTTTAGCCTGCAAAGCGCCGGGCGCTTTGTCGACAAACTACCGGCAGAGCCGGAGCAGAATATCGTTTATCAATGCTGGCAGCGTTTTTGCGAGGCGGTGGGGGAAACGGTGCCGGTCGCCATGCTACTGGAAAAAAATATGCCCATTGGCTCCGGTCTGGGCTCCAGCGCCTGTTCGGTGGTGGTGGCGCTGGTAGCGATGAATGCCCATTGCGGCCGCCCGCTAAACGATGATCAGATGCTGATGCTGATGGGGGAAATGGAGGGGCGCATTTCCGGCGGGGTGCATTTCGATAATGTCGCACCCTGTTTTCTCGGCGGCATGCAGTTGATGCTTGAGGAAAACGGCATCATCAGCCAGACGGTGCCGGGGTTTGACGACTGGCTGTGGGTGATGGCCTATCCGGGCATCAAAGTGAGCACCGCCGAGGCGCGGGCGATTCTGCCGGCACAATATCGTCGCCAGGACTGCATCAGCCATGGCCGTTATCTGGCGTGCTTTGTGCACGCCTGCCATACCCGTCAGCCGGCGCTTGCGGCTAAACTGATGAAAGATGTTATCGCCGAGCCCTATCGCACCCGACTGCTGCCGGGCTTCGCCGATGCGCGCCAGGCGGTGGGCGATATCGGCGCGCTGGCCTGTGGTATCTCGGGTTCGGGACCAACGCTATTCGCTATCTGCGATCGCCAGGACACCGCGTCGCGCGTCGCCGACTGGCTGACGCAGCACTACCTGCAAAACGACGAAGGTTTTGTTCATATTTGCCGCCTGGATACCTCCGGTGCCCGTTTGATGATGGAT
;
END;