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Phylomatic: add 'random placement' function #2

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camwebb opened this issue May 31, 2012 · 0 comments
Open

Phylomatic: add 'random placement' function #2

camwebb opened this issue May 31, 2012 · 0 comments
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@camwebb
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camwebb commented May 31, 2012

Goal

Rather than collapsing a node in which some taxa are not directly matched, fit the unplaced taxa into the tree at random points

Algorithm

  1. In existing, non-polytomous clade, add unmatched taxon at a random node

Rationale

Need to explore this: is attaching a taxon to a random inner node the appropriate action? Test it:

  1. Make random tree
  2. Pick one terminal taxon at random
  3. For the node N to which this taxon attaches, output the depth D of N and node number N, and total number of nodes T in the tree
  4. Repeat from (1) 1,000 times
  5. Hopefully the distributions of D and N/T are both uniform
@ghost ghost assigned camwebb May 31, 2012
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