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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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Revision as of 00:39, 19 January 2010

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 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