How to show trees in increasing order ?

[Sid S]

Hi all,

Is it possible to show the BioGeoBEARS output in increasing order as attached in the figure from this paper

https://doi.org/10.1016/j.ympev.2015.10.001

Regards,

Sid. 

[Sid S]

Re-forwarding for solution 

[Nick Matzke]

Hiya,

If by "increasing order", you mean a ladderized tree, the method would be:

1. Ladderize your tree with the ape function ape::ladderize()

plot(tr)

tr2 = ape::ladderize(phy=tr, right=TRUE)

plot(tr2)

2. Save out to a new .newick file

3. Re-run BioGeoBEARS analysis on the ladderized tree, or (if that is too slow), there is a function somewhere that can transfer results on an old tree to a reordered tree. I would have to go find it though.

(reordered tree = tree with the same clades and topology, but with some nodes rotated for visual purposes, e.g. ladderizing or some other configuration)

Cheers,

Nick

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