手把手教你构建系统发育树.

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
Construction of Phylogenetic Tree
Extraction of chromosomal DNA PCR amplification of the16S rRNA gene
Assmbly of 16S rRNA gene fragments
Obtain closely related sequences
74
31
35
49
Nocardiopsis composta DSM 445பைடு நூலகம்1T 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
YIM 90008
28 96 62 92 100
Nocardiopsis salina KCTC 19003T AY373031 Nocardiopsis xinjiangensis DSM 44589T AF251709
Nocardiopsis litoralis DSM 45168T EU583726
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
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
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
EzTaxon http://147.47.212.35:8080/
OR
RDP(RIBOSOMAL DATABASE PROJECT) homepage http://www.bacterio.cict.fr/
Multiple-sequences alignments
TOOL---CLUSTAL_X
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
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)
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/
YOU NEED A REGISTRATION NUMBER TO LOG IN THIS PAGE FIRST
38 89 40
Nocardiopsis listeri DSM 40297T X97887 Nocardiopsis alba DSM 43377T X97883 Nocardiopsis tropica DSM 44381T AF105971
99
Nocardiopsis umidischolae DSM 44362T AY036001