Dear Forum,
I have a list containing sampled trees for the same "taxa" and would
like to plot their consensus tree
with the support values (absolute numbers or frequencies) for the
various branches.
(as done by the Consense program of the Phylip suite)
I understand that boot.phylo() returns an object "bs" that contains such
information as bs$BP.
My scenario is similar, but the sampled trees are not based on sequence
information and boot.phylo()
is not applicable here.
I assume the support values can be obtained from prop.part(), but I
could not figure how.
Thank you for any help or suggestions,
Thomas
#tr is list of trees
ct<-consensus(tr, p=0.5) # majority consensus
pt<-prop.part(tr)
pc<-prop.part(ct)
# calculate support values
sv <- f(pc, pt) = ???
plot(ct); nodelabels(sv)
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