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Difference between revisions of "Mgcluster"

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The [[mgcluster]] command ....
 
The [[mgcluster]] command ....
  
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For this tutorial you should download the ..... file and decompress it.
  
 
__TOC__
 
__TOC__
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===method===
 
===method===
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* [[Nearest neighbor]]: Each of the sequences within an OTU are at most X% distant from the most similar sequence in the OTU.
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* [[Furthest neighbor]]: All of the sequences within an OTU are at most X% distant from all of the other sequences within the OTU.
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* [[Average neighbor]]: This method is a middle ground between the other two algorithms.
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  cluster method: furthest, nearest or average.  
 
  cluster method: furthest, nearest or average.  
 
default = furthest
 
default = furthest

Revision as of 18:24, 27 January 2010

The mgcluster command ....


For this tutorial you should download the ..... file and decompress it.


Default settings

The blast parameter is required...

mgcluster(blast=bap.100.blast)

Options

name

mgcluster(blast=bap.100.blast, name=bap.100.names)

method

  • Nearest neighbor: Each of the sequences within an OTU are at most X% distant from the most similar sequence in the OTU.
  • Furthest neighbor: All of the sequences within an OTU are at most X% distant from all of the other sequences within the OTU.
  • Average neighbor: This method is a middle ground between the other two algorithms.
cluster method: furthest, nearest or average. 

default = furthest

cutoff

default = 0.70
mgcluster(blast=bap.100.blast, cutoff=1.0)

precision

default = 100

merge

Default = true, meaning merge after clustering mgcluster(blast=bap.100.blast, merge=f)

min

default = true, meaning use minimum blast score ratio
mgcluster(blast=bap.100.blast, min=f)

length

default = 5, minimum overlap

mgcluster(blast=bap.100.blast, length=10)


penalty

default = 0.10

mgcluster(blast=bap.100.blast, penalty=0.15)

hcluster

default = false, meaning don't use hcluster, use cluster.
mgcluster(blast=bap.100.blast, hcluster=t)