Hello Users, I have a question regarding midpoint rooting with Phangorn and how it is dealing with branch lengths. I read in a tree and after midpoint rooting and calculating the wRFdist, I get a very small value, which, I figured out after looking at the edge lengths for both the trees that midpoint rooting modifies the branch lengths at the root (subtracts from one and adds to the other). Is it appropriate to be doing that? Below is my code and example. I apologize if I am not clear in my question.
> set.seed(42)
> tree<-read.tree("tree_mod1_1.nwk")
> New_tree<-midpoint(tree)
> wRF.dist(tree,New_tree,rooted=T)
[1] 0.000000007255
midpoint root (New_tree)
0.002071788627500 51 52
0.000603571372500 51 75
true tree (tree)
0.00207178500000000000 51 52
0.00060357500000000000 51 75
Thanks,
Lavanya
tree_mod1_1.nwk
Description: Binary data
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