Just to add to Juan's comment, for most analyses where you need branch
lengths, you need them to be fairly accurate (but not all, so his is useful
advice for those cases). In cases where you do need good branch lengths
(diversification, ancestral state reconstruction, phylogenetic diversity,
rates
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The "strange" shape of your tree seems to result from negative
branch lengths.
If your goal is to just obtain an ultrametric tree under no specific
assumptions, use
compute.brtime (yourtree, method="coalescent", force.positive=TRUE).
Where 'yourtree' m
Dear all,
I just started to work with R and I have the following problem:
I calculated a phylogenetic tree in RAmML. For further analysis, I need
an ultrametric tree which
I wanted to make with the chronoMPL command in APE.
However, the tree was not dichotomous and I used the multi2di(phylogeny