Hi all,
I'm trying to decide if this an R error, or an error in
how I've implemented branch lengths.
When i create the cophenetic matrix for my tree, and look at the
relatedness of all tips to a single tip (i.e just looking at one column in
the matrix). I find that a large portion of them have identical cophenetic
distances.
I thought the cophenetic would be the sum of the branch length between
tips (patristic distance), therefore there should only be pairs (sister
species have equal terminal branch length) with *exactly * the same value.
Comparisons from distantly related taxa should be similar, since most of
the distance is dictated by the internal branches, but the terminal branch
should atleast create some difference.
Sorry that i can't really create a reproducible example for the question.
Here is some documentation:
trx<-read.nexus("ColombiaPhylogenyUM.tre")
seeds<-sample(trx$tip.label,1)
sp.weight.alpha<-cophenetic(trx)[,seeds]
> table(sp.weight.alpha)sp.weight.alpha
0 0.00775074 0.1179723 0.2187406 0.2379734 0.23797341 0.2525792
1 1 2 4 3 2 6
0.36612256 0.36612257 0.52326843 0.59034104 0.59034105 0.59034106 0.607038
2 2 2 31 82 29 3
82 of the species have the exact same distance to my selected tip .59034105
Am i using this function correctly?
I appreciate the help,
Ben Weinstein
--
Ben Weinstein
Graduate Student
Ecology and Evolution
Stony Brook University
http://life.bio.sunysb.edu/~bweinste/index.html
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