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Difference between revisions of "Phylogenetic diversity"

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(New page: ==inputs== ===required=== * tree with branch lengths ===optional=== * name file * rarefy = T/[F] * freq = 100 * group file ==method== default - calculate the branch length in a tree (as ...)
 
 
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==inputs==
 
==inputs==
 
===required===
 
===required===
* tree with branch lengths
+
* run read.tree command
  
 
===optional===
 
===optional===
* name file
+
 
 
* rarefy = T/[F]
 
* rarefy = T/[F]
 
* freq = 100
 
* freq = 100
* group file
+
* iters - if rarefy
 +
* groups - select specific groups
  
 
==method==
 
==method==

Latest revision as of 12:53, 4 May 2010

inputs

required

  • run read.tree command

optional

  • rarefy = T/[F]
  • freq = 100
  • iters - if rarefy
  • groups - select specific groups

method

default - calculate the branch length in a tree (as a fraction of the total number of sequences???) in the tree rarefy=T - perform pd calculation by starting with an empty tree and adding each sequence (based on freq). keep track of pd as a function of sampling effort and produce rarefaction data group - because each tree might represent numerous groups of sequences, the group file will perform calculations for each group separately name - a tree may only represent the unique sequences and the name file would bring in the redundant names