Hi Monica,
Perhaps it's because your bootstrap values are stored as node labels, instead 
of edge labels. This problem is well documented here:
https://doi.org/10.1093/molbev/msx055
But perhaps it's a different issue in your case.
C├ęcile

On Jun 24, 2017, at 9:18 AM, Monica Carlsen 
<anthuriumb...@gmail.com<mailto:anthuriumb...@gmail.com>> wrote:

Hi everyone,

I have a set of gene trees (resulting from RAxML) analyses that I would like to 
manipulate before inputting them into a coalescence analysis.

I have unrooted trees with bootstrap support as node labels. I would need to 
collapse branches with less than 50%BS, and root these trees.

I'm using a combination of packages (ape, phytools, phangorn) to achieve these 
results. When visualizing the trees (using ggtree), I noticed that the order of 
the steps makes a difference in the final output tree. See attached script, 
dataset and tree comparison PDF.

For example (in PDF), if I collapse branches first, then root the tree, I get 
tree # 3. But, if I do the rooting first, then collapsing branches, I get tree 
# 4, as well as warnings that "number of items to replace is not a multiple of 
replacement length" in some steps. Tree #1 is the original tree, unrooted, 
uncollapsed, straight from RAxML. Tree # 2 is the collapsed, but unrooted tree.

The differences in topology are so striking that they influence (a lot!) the 
final topology and support of the coalescence analysis.

I've read before that different software plots/uses the support-as-node-label 
in different ways, and that could create erroneous representations. But, I 
can't seem to understand which one is the correct one in my case.

Any thoughts on what could be happening here? what would be the order in which 
the steps should be performed? or any recommendations for different packages to 
use that could solve the issue?

Monica.

Monica Carlsen, PhD - Plant systematics, ecology and evolution
Peter Buck Postdoctoral Fellow | Smithsonian National Museum of Natural History 
| Washington, D.C.
Research Associate | Missouri Botanical Garden | St. Louis, MO

<MayTrees.txt>
<Rplot11.pdf>
<TreeComparisons.R>
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