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进化树构建-NJ 法 V1
2012-05-17 | 阅:  转:  |  分享 
  
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ByZHAOYangguo,email:sunshine.zhao@yahoo.com.cn



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>Eu-b1

AGAGTTTGATCCTGGCTCAgGATGAACGCTGGCGGCGTGCTTAACACATGCAA

GTCGAACgCGAAAGGGACTTCGGTCCTGAGTAAAGTGGCGCACGGGTGAGTA

ACGCGTAGATAACCTGTCTTTGTGTCTGGAATAATACTTCGAAAGGGGTACTAA

TACCGGATAACCTTGCTTTTCACAAGTTATGCAAGCAAAGGTGGCCTCTGATAC

AAGCTACTGCATGAAGAGGGGTCTGCGTACCATTAGCTAGTAGGTGGGGTAATG

GCCTACCTAGGCGACGATGGTTAGCGGGTCTGAGAGGATGATCCGCCACACTG

GCACTGGAACACGGGCCAGACTCCTACGGGAGGCAGCAGTGAGGAATATTGC

GCAATGGGGGCAACCCTGACGCAGCGACGCCGCGTGAGTGAGGAAGGCCTTC

GGGTCGTAAAGCTCTGTCAAGAGGAAAGAAGTGCATAATGGTTAATACCTGTTA

TGTTTGACGGTACCTCTAAAGGAAGCACCGGCTAACTCCGTGCCAGCAGCCGC

GGTAA

>Eu-b2

AGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAA

GTCGAGCGGATGAGAAGAGCTTGCTCTTCGATTCAGCGGCGGACGGGTGAGTA

ATACCTAGGAATCTGCCTGGTAGTGGGGGACAACGTTTCGAAAGGAACGCTAA

TACCGCATACGTCCTACGGGAGAAAGCAGGGGACCTTCGGGCCTTGCGCTATC

.&(" .PMFDVMBS&WPMVUJPOBSZ(FOFUJDT"OBMZTJT


5IFTPGUXBSFJTBOJOUFHSBUFEUPPMGPSBVUPNBUJDBOENBOVBMTFRVFODF

BMJHONFOU
JOGFSSJOHQIZMPHFOFUJDUSFFT
NJOJOHXFCCBTFEEBUBCBTFT


FTUJNBUJOHSBUFTPGNPMFDVMBSFWPMVUJPO
BOEUFTUJOHFWPMVUJPOBSZ

IZQPUIFTFT

2

AGATGAGCCTAGGTCGGATTAGCTAGTTGGTGAGGTAATGGCTCACCAAGGCT

ACGATCCGTAACTGGTCTGAGAGGATGATCAGTCACATTGGAACTGAGACACG

GTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAA

GCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCAC

TTTAAGTTGGGAGGAAGGGCATTAACCTAATACGTTAGTGTTTTGACGTTACCG

ACAGAATAAGCACCGGCTAACTCTGTGCCAGCAGCCGCGGTAA

&·&·&·&·&·&·&·&·&·&·&·&·&·&·&·&·&·&·&·&·&·&·&·&·&·&·&·&·&·&·&·&·&·&·&·&·







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>Eu-b1

AGAGTTTGATCCTGGCTCAgGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAAC

gCGAAAGGGACTTCGGTCCTGAGTAAAGTGGCGCACGGGTGAGTAACGCGTAGATAACC

TGTCTTTGTGTCTGGAATAATACTTCGAAAGGGGTACTAATACCGGATAACCTTGCTTTTC

ACAAGTTATGCAAGCAAAGGTGGCCTCTGATACAAGCTACTGCATGAAGAGGGGTCTGC

GTACCATTAGCTAGTAGGTGGGGTAATGGCCTACCTAGGCGACGATGGTTAGCGGGTCTG

AGAGGATGATCCGCCACACTGGCACTGGAACACGGGCCAGACTCCTACGGGAGGCAGC

AGTGAGGAATATTGCGCAATGGGGGCAACCCTGACGCAGCGACGCCGCGTGAGTGAGG

AAGGCCTTCGGGTCGTAAAGCTCTGTCAAGAGGAAAGAAGTGCATAATGGTTAATACCT

GTTATGTTTGACGGTACCTCTAAAGGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGT

AA

>gi|45238864|gb|AY548775.1|Desulfobulbussp.RPf35L1716SribosomalRNAgenegene,partial

sequence

TTGATCCTGGCTCAGAACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGCG

AAAGGGACTTCGGTCCTGAGTAAAGTGGCGCACGGGTGAGTAACGCGTAGATAACCTG

TCTTCATGTCTGGAATAATACGCCGAAAGGGGTACTAATACCGGATATTCTTGCTTTTC

ATAAGTTATGCAAGCAAAGGTGGCCTCTGCATATGCTACTGCATGAAGAGGGGTCTGC

GTACCATTAGCTAGTAGGTGGGGTAATGGCCTACCTAGGCGACGATGGTTAGCGGGTC

TGAGAGGATGATCCGCCACACTGGCACTGGAACACGGGCCAGACTCCTACGGGAGGC

AGCAGTGAGGAATATTGCGCAATGGGGGAAACCCTGACGCAGCGACGCCGCGTGAGT

GAGGAAGGCCTTCGGGTCGTAAAGCTCTGTCAAGAGGAAAGAAGTGTACAATGGCTA

ATACCTGTTGTATTTGACGGTACCTCTAAAGGAAGCACCGGCTAACTCCGTGCCAGCA

GCCGCGGTAATACGGAGGGTGCAAGCGTTGTTCGGAATCACTGGGCGTAAAGGGCGCG

TAGGCGGCTTGGTAAGTCAGATGTGAAAGCCCACGGCTTAACTGTGGAAGTGCATTTG

AAACTGTCAGGCTTGAGTACCAGAGGGGAAAGTGGAATTCCCGGTGTAGAGGTGAAAT

TCGTAGATATCGGGAGGAATACCGGTGGCGAAGGCGACTTTCTGGCTGGATACTGACG

CTGAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCTGT

AAACGATGTGAACTAGATGCAGGGGGTGTTGATCCCTTCTGTGTCGCAGCTAACGCAT

TAAGTTCACCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGGGG

GCCCGCACAAGCGGTGGAGTATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCT

GGTCTTGACATCCCGGAAATCTTTTGGAAACAAGAGAGTGCTTCCATTCGGAAGAATC

TGGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCC

CGCAACGAGCGCAACCCTTGCCTTTAGTTGCCAGCAGTTCGGCTGGGCACTCTAAAGG

GACTGCCGGTGTTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCTTTA

TGACCAGGGCTACACACGTACTACAATGGCCGATACAAAGGGCAGCGACACTGCGAG

GTGGAGCCAATCCCATAAAATCGGTCTCAGTCCGGATTGGAGTCTGCAACTCGACTCC

ATGAAGTTGGAATCGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGG

GCCTTGTACACACCGCCCGTCACACCACGGGAGTCGGTTGTACCAGAAGCAGTTGAGC

TAACCGCAAGGGGGCAGGCTGCCAAGGTATGGCTGGTAACTGGGGTGAAGTCGTAAC

AAGGTAACCGTA

>Eu-b2

5

AGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAG

CGGATGAGAAGAGCTTGCTCTTCGATTCAGCGGCGGACGGGTGAGTAATACCTAGGAAT

CTGCCTGGTAGTGGGGGACAACGTTTCGAAAGGAACGCTAATACCGCATACGTCCTACG

GGAGAAAGCAGGGGACCTTCGGGCCTTGCGCTATCAGATGAGCCTAGGTCGGATTAGCT

AGTTGGTGAGGTAATGGCTCACCAAGGCTACGATCCGTAACTGGTCTGAGAGGATGATCA

GTCACATTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATT

GGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATT

GTAAAGCACTTTAAGTTGGGAGGAAGGGCATTAACCTAATACGTTAGTGTTTTGACGTTA

CCGACAGAATAAGCACCGGCTAACTCTGTGCCAGCAGCCGCGGTAA

>gi|62465604|gb|AY972175.1|PseudomonasputidastrainP1916SribosomalRNAgene,partial

sequence

CCTGTTTTGCATGCCGTCCCAAGCGGTCACTTAATGCGTTAGCTGCGCCACTAAAATCTC

AAGGATTCCAACGGCTAGTTGACATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCT

GTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATCAGTCCAGGTGGTCGCCTTCGCC

ACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCT

ACCGTACTCTAGCTTGCCAGTTTTGGATGCAGTTCCCAGGTTGAGCCCGGGGCTTTCACA

TCCAACTTAACAAACCACCTACGCGCGCTTTACGCCCAGTAATTCCGATTAACGCTTGCA

CCCTCTGTATTACCGCGGCTGCTGGCACAGAGTTAGCCGGTGCTTATTCTGTCGGTAACG

TCAAAACACTAACGTATTAGGTTAATGCCCTTCCTCCCAACTTAAAGTGCTTTACAATCC

GAAGACCTTCTTCACACACGCGGCATGGCTGGATCAGGCTTTCGCCCATTGTCCAATATT

CCCCACTGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGACTGATCAT

CCTCTCAGACCAGTTACGGATCGTCGCCTTGGTGAGCCATTACCTCACCAACTAGCTAAT

CCGACCTAGGCTCATCTGATAGCGCAAGGCCCGAAGGTCCCCTGCTTTCTCCCGTAGGA

CGTATGCGGTATTAGCGTTCCTTTCGAAACGTTGTCCCCCACTACCAGGCAGATTCCTAG

GCATTACTCACCCGTCCGCCGCTGAATCGAAGAGCAAGCTCTTCTCATCCGCTCGACTTG

CATGTGTTAGGCCTGCCGCCAGCGTTCAATCTGAGCCAGGATCAAACTCTGTTGCTAAA

AAAAATTCCCGGA

>E.coli-M25588,? I?


AAATTGAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAA

GTCGAACGGTAACAGCAGAAGGGCTTGCTGCTTTTGACGCTGGACGGCGAGTGTGTAA

TGTCTGGGAAACTGCCTGGGGGGAGATGATAACACTTGGAAACGGTAGCTAATACGTGC

ATAATGTCGCAAGACCGAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGCCCAGA

TGGGATTAGGGGTAGCTAGTAACGAGTGGCTCACCTAGGCGACGATTCCAGCTGGTCTG

AGAGGGATGACCAGCACCACTGGAACTGAGACACGGTCCAGACTCCTACGGGGGCAGC

AGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGTGCCGTATGAAGGAA

GCCTTCGGGTTGTGAAGGGAGTAAAGTCTAATACTTTGCTCATTGTTACCCGACGCAGC

GAAGAAGCCACGTACTTTCAGCGAGAGAAGGGGGGGTGGCTAACTCCGTGCCAGCAGC

CGCGGTAATACGAGGTTAATCGCAAGCGTGGGCGGAATTACTGTAAAGCACGAGCGCCT

GGTTTGTTAAGTCAGATGTGAAATCCCCGGGCCTAACCCTGGGAACTGCATCTGATACTG

GCAAGCTTGTAGGTCTCGGAGAGGTAGAATTCCAGTAGAGATCTGGGGAATACCGGTGG

CGGAAGCCCCCCTGGCGGACTGACGAAAGCTCAGGTGTGCGGGGGCATACTCCGCCGG

TAGTCCACGTAAACGATGTCGTGGGGTGACTTGCCCCTTGAGGCGTGGCCTTCGAGGCG

CTAACGTTAAGTCGCCTGACCCGGGGGGGTACGCCGCAAGGTTAAAACTCAAATCGAAT

TGGGGGCCCGGAGCACAAGACGCATGATGTGCGTTTAATTCGCAACGAAGAACCTTACC

TGGTCTTGACCATCACGGAAGTGTTTTCAGAGATGAGAATGTGCTTCCGGGAACCGAGA

CAGCTGCATGGCTGTCAGGTCGTGTTGTGTTGCGAAATGGGTCCCGTTAAGTTGCCTGC

6

AACGAGCAACCCTTATCCTTTGTTGCCAGCGGGAACTCAAAGAGAGACTGCCAGCCGT

CCGTGGATTAAACGAGGGGGGGAAGTGGGGATGACGTCAAGTCATCATGGCCCCCTTCA

CGACCAGGGCACACACTGTGCTACAATGGCGCATCACAAAGAGAGCGACTCCCGCGAG

AGCAAGCGGATCTCATAAAGTCGTGCGTAGTCTGAGGTCCGGATTGCTAACCGACTCCA

TGAAGTCGGAATCGCTAGTGTAATCGGATCCAGAATGCACCGGTGAATACGTTCCCGGG

CCTTGTACACACGCCCCGTCACACCATGGGGTGGAGGTGACTGTGGGTTGATATTCGTC

CAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCTTACCACTTTGTCGTAACAAGGTAA

CCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA





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Eu-b1

gi|45238864|gb|AY548775.1|Desulfobul...

Eu-b2

E.coli-M25588

gi|62465604|gb|AY972175.1|Pseudomona...











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