Question: identifying bipartitions in tree
0
gravatar for sam
4.3 years ago by
sam0
United States
sam0 wrote:

I have a bipartition from tree(a) where only one single mutation hits a specific edge of the (converts 0 to 1 - infinite sites model) and affecting all the descendants of this edge with the mutation 1. For example I might end up with the following bipartition: {A,B,C} | {D,E} where A, B, C, D, and E are leaf labels (taxa).

I'm interested in identifying whether the aforementioned bipartition is compatible with tree(b). In other words, I want to identify whether tree(b) contains that bipartition. Is there any package in R that could assist in doing this?

R • 1.1k views
ADD COMMENTlink modified 4.3 years ago by Brice Sarver2.6k • written 4.3 years ago by sam0
1
gravatar for Brice Sarver
4.3 years ago by
Brice Sarver2.6k
United States
Brice Sarver2.6k wrote:

The

subtrees() 

function in ape will return all subtrees given a phylogenetic tree. You can then use simple tree distances or string matching to see whether or not your subtree of interest exists in the list of subtrees. This is the easiest way I've found to do this absent a function in a package that combines both steps into a single call.

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Brice Sarver2.6k
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