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Problem getting tree bipartitions

I wanted to get all the bipartitions from a tree: tree image

It should give the following bipartitions:

  1. A,B,C,D,E,F,G,H
  2. A,B,C,D,I,J
  3. E,F,G,H,I,J
  4. A,B,C,D
  5. E,F,G,H
  6. A,B
  7. C,D
  8. E,F
  9. G,H
  10. I,J

However, when I did the following:

library('ape')    
t = read.tree('((((A,B),(C,D)),((E,F),(G,H))),(I,J));') 
prop.part(t)

or

library('ape')    
t = read.tree('((((A,B),(C,D)),((E,F),(G,H))),(I,J));') 
subtrees(t)

they only gave me the bipartitions 1,4-10, without 2 and 3.

What is the problem here?

r phylogeny tree phylo ape

1 answer

Hello,

prop.part() splits the set of labels (taxa) into two non-empty subsets, e.g.

A,B,C,D,I,J | E,F,G,H

or

A,B,C,D | E,F,G,H,I,J

In your list 2. and 5. (3. and 4.) refer to the same partition.

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