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Difference between revisions of "Otu.hierarchy"

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Line 23: Line 23:
 
  AY457697,AY457787 AY457697 AY457787
 
  AY457697,AY457787 AY457697 AY457787
 
  ...
 
  ...
 +
 +
 +
The first column is what the OTU looked like at distance 0.35 followed by the list of OTUs at distance 0.03 that merged.
 +
  
 
==Options==
 
==Options==
Line 29: Line 33:
  
 
  mothur > otu.hierarchy(list=abrecovery.fn.list, label=0.03-0.35, output=number)
 
  mothur > otu.hierarchy(list=abrecovery.fn.list, label=0.03-0.35, output=number)
 
 
The first column is what the OTU looked like at distance 0.35 followed by the list of OTUs at distance 0.03 that merged.
 

Revision as of 13:35, 20 April 2010

The otu.hierarchy command relates OTUs at different distances



Default settings

A list file and two labels must be inputted for otu.hierarchy to be successful.

mothur > otu.hierarchy(list=abrecovery.fn.list, label=0.03-0.35)

The abrecovery.fn.0.03-0.35.otu.hierarchy output file will look like:

...
AY457705	AY457705	
AY457724	AY457724	
AY457722	AY457722	
AY457703	AY457703	
AY457720,AY457728,AY457746,AY457742,AY457781	AY457781	AY457742	AY457720,AY457728,AY457746	
AY457713,AY457719	AY457719	AY457713	
AY457712	AY457712	
AY457681,AY457819,AY457727	AY457727	AY457681,AY457819	
AY457697,AY457787	AY457697	AY457787	
...


The first column is what the OTU looked like at distance 0.35 followed by the list of OTUs at distance 0.03 that merged.


Options

The output parameter allows you to either specify the output to display the names of the sequences in the otus or the otu numbers, the default is name.

mothur > otu.hierarchy(list=abrecovery.fn.list, label=0.03-0.35, output=number)