手把手教你构建系统发育树

74
31
35
49
Nocardiopsis comቤተ መጻሕፍቲ ባይዱosta DSM 44551T AF360734
Nocardiopsis potens DSM 45234T FM253114
42 99 91
Nocardiopsis chromatogenes DSM 44844T AY619715
Nocardiopsis baichengensis DSM 44845T AY619716 Nocardiopsis halophila DSM 44494T AJ421018 Actinomadura echinospora DSM 43163T AJ420135
Phylogenetic analysis & Bootstrap analysis
TOOLS
MEGA-----UPGMA\NJ\MP\ME
PHYLIP----NJ\MP\ML
Example 1 MEGA--------NJ
Example MEGA ---------NJ
99 68 88 65
Nocardiopsis exhalans DSM 44407T AY028325
Nocardiopsis valliformis DSM 45023T AY336503
Nocardiopsis metallicus DSM 44598T AJ420769 Nocardiopsis ganjiahuensis DSM 45031T AY336513 Nocardiopsis alkaliphila DSM 44657T AY230848
Nocardiopsis listeri DSM 40297T X97887 924 Nocardiopsis alkaliphila DSM 44657T AY230848 Nocardiopsis alba DSM 43377T X97883 umidischolae DSM 44362T AY036001 tropica DSM 44381T AF105971 synnemataformans DSM 44143T Y13593 dassonvillei subsp. albirubida DSM 40465T X97882 dassonvillei subsp. dassonvillei DSM 43111T X97886
Outtree
intree
CONSENSE.EXE
NJ TREE
631 364 417
Nocardiopsis valliformis DSM 45023T AY336503
994 695 875
Nocardiopsis exhalans DSM 44407T AY028325 Nocardiopsis metallicus DSM 44598T AJ420769 Nocardiopsis ganjiahuensis DSM 45031T AY336513
568
Nocardiopsis halotolerans DSM 44410T AJ290448 Nocardiopsis rosea DSM 44842T AY619713
1000
973 995 446 994
Nocardiopsis rhodophaea DSM 44843T AY619714 Nocardiopsis gilva DSM 44841T AY619712 Nocardiopsis baichengensis DSM 44845T AY619716
38 89 40
Nocardiopsis listeri DSM 40297T X97887 Nocardiopsis alba DSM 43377T X97883 Nocardiopsis tropica DSM 44381T AF105971
99
Nocardiopsis umidischolae DSM 44362T AY036001
CONSENSE.EXE
DNAPARS.EXE TREEVIEW.EXE
MP TREE
Nocardiopsis 866 Nocardiopsis 554 550 Nocardiopsis Nocardiopsis 787 581
exhalans DSM 44407T AY028325 valliformis DSM 45023T AY336503 metallicus DSM 44598T AJ420769 ganjiahuensis DSM 45031T AY336513
YIM 90008
28 96 62 92 100
Nocardiopsis salina KCTC 19003T AY373031 Nocardiopsis xinjiangensis DSM 44589T AF251709
Nocardiopsis litoralis DSM 45168T EU583726
Multiple alignments
Phylogenetic analysis
Bootstrap analysis
Assmbly of 16S rRNA gene
TOOL ---SeqMan(DNASTAR)
Select your sequences here
R
A
Delete it
Obtain closely related sequences
TOOLS
NCBI RDP http://www.ncbi.nlm.nih.gov/ http://www.bacterio.cict.fr/
EzTaxon http://147.47.212.35:8080/
NCBI homepage http://www.ncbi.nlm.nih.gov/
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Nocardiopsis listeri DSM 40297T X97887
918
Nocardiopsis alkaliphila DSM 44657T AY230848 Nocardiopsis alba DSM 43377T X97883 Nocardiopsis tropica DSM 44381T AF105971
EzTaxon http://147.47.212.35:8080/
OR
RDP(RIBOSOMAL DATABASE PROJECT) homepage http://www.bacterio.cict.fr/
Multiple-sequences alignments
TOOL---CLUSTAL_X

102 264 408
323
Nocardiopsis 996 Nocardiopsis Nocardiopsis 482 Nocardiopsis 588 62 Nocardiopsis
Nocardiopsis lucentensis DSM 44048T X97888 Nocardiopsis aegyptia DSM 44442T AJ539401 Nocardiopsis quinghaiensis DSM 44739T EF597511 526 Nocardiopsis halotolerans DSM 44410T AJ290448 Nocardiopsis 997 Nocardiopsis 961 Nocardiopsis 913 Nocardiopsis 611 YIM 90008 Nocardiopsis 926 Nocardiopsis 851 Nocardiopsis 515 Nocardiopsis 628 Nocardiopsis 422 Nocardiopsis 981 Nocardiopsis 308 988 Nocardiopsis 542 Nocardiopsis litoralis DSM 45168T EU583726 kunsanensis DSM 44524T AF195412 xinjiangensis DSM 44589T AF251709 salina KCTC 19003T AY373031 halophila DSM 44494T AJ421018 baichengensis DSM 44845T AY619716 chromatogenes DSM 44844T AY619715 potens DSM 45234T FM253114 composta DSM 44551T AF360734 rhodophaea DSM 44843T AY619714 rosea DSM 44842T AY619713 gilva DSM 44841T AY619712 arabia DSM 45083T EF095149
Phylogenetic analysis & Bootstrap analysis
METHODS
Distance-based method Maximum parsimony method (MP) Maximum likehood method(ML)
Unweightedpair group method with arithmetic mean(UPGMA) Neighbor joining(NJ) Minimum evolution(ME)
928
Nocardiopsis halophila DSM 44494T AJ421018 Nocardiopsis chromatogenes DSM 44844T AY619715
328
Nocardiopsis composta DSM 44551T AF360734
752
510
Nocardiopsis potens DSM 45234T FM253114 Nocardiopsis trehalosi DSM 44380T AF105972
Nocardiopsis kunsanensis DSM 44524 AF195412
99 17 27 80 81
Nocardiopsis aegyptia DSM 44442T AJ539401 Nocardiopsis lucentensis DSM 44048T X97888 Nocardiopsis dassonvillei subsp. dassonvillei DSM 43111T X97886 Nocardiopsis dassonvillei subsp. albirubida DSM 40465T X97882 Nocardiopsis synnemataformans DSM 44143T Y13593 Nocardiopsis quinghaiensis DSM 44739T EF597511
57
Nocardiopsis halotolerans DSM 44410T AJ290448 Nocardiopsis trehalosi DSM 44380T AF105972
95 99
Nocardiopsis rhodophaea DSM 44843T AY619714 Nocardiopsis rosea DSM 44842T AY619713 Nocardiopsis gilva DSM 44841T AY619712 Nocardiopsis arabia DSM 45083T EF095149
1000 278
Nocardiopsis umidischolae DSM 44362T AY036001 Nocardiopsis litoralis DSM 45168T EU583726
1000 917 607 962
Nocardiopsis kunsanensis DSM 44524T AF195412 Nocardiopsis xinjiangensis DSM 44589T AF251709 Nocardiopsis salina KCTC 19003T AY373031
Construction of Phylogenetic Tree
Extraction of chromosomal DNA PCR amplification of the16S rRNA gene
Assmbly of 16S rRNA gene fragments
Obtain closely related sequences
335
Nocardiopsis arabia DSM 45083T EF095149 Actinomadura echinospora DSM 43163T AJ420135
Example3 PHYLIP-----MP
BIOEDIT SEQBOOT DNAPARS CONSENSE TREEVIEW
0.01
Example2
PHYLIP---NJ
BIOEDIT SEQBOOT DNADIST NEIGHBOR CONSENSE TREVIEW
A number= 4n+1>0
SEQBOOT.EXE
Outfile
infile
DNADIST.EXE
Outfile
infile
NEIGHBOR.EXE
290
YIM 90008
Nocardiopsis dassonvillei subsp. albirubida DSM 40465T X97882
811 815 995 258 169
Nocardiopsis synnemataformans DSM 44143T Y13593 Nocardiopsis dassonvillei subsp. dassonvillei DSM 43111T X97886 Nocardiopsis lucentensis DSM 44048T X97888 Nocardiopsis aegyptia DSM 44442T AJ539401 Nocardiopsis quinghaiensis DSM 44739T EF597511