How does ggtree interprets branch support value (e.g bootstrap value) given as node label?

Question

[Chirag Parsania]

Hi,

I came across the paper describing issues interpreting phylogenetic tree due to branch support given as node label in newick format.

Let me describe the problem very briefly, which is explained in depth in the paper given above. Many tree output programmes gives branch support values (e.g bootstrap value) as node label. However, many tree manipulation softwares interpret node labels as node labels and not branch support values. Therefore, while rerooting the tree it misplace the branch support values, which leads to different tree interpretation.

I wonder, how ggtree addresses this issue ? below, I explained the situation with example

library("ggtree")
## random tree with random bootstap values given as node label in newick format 
sample_tree <- read.tree(text = "((C,D)90,(A,(B,X)95)100,E)85;")

## reroot from E 
reroot_e <- root(phy = sample_tree , outgroup = "E") 
ggtree(reroot_e)+ geom_tiplab(size = 7, col ="blue") +geom_nodelab(size = 7, col= "red") + theme_tree2() +  xlim(0,4.5)

## reroot the tree from X 
re_root_x <- root(phy = sample_tree , outgroup = "X")
ggtree(re_root_x)+ geom_tiplab(size = 7, col ="blue") +geom_nodelab(size = 7, col= "red") + theme_tree2() + xlim(0,4.5)

I wonder,are these trees have same bootstrap interpretation or they are different ??

@Guangchuang Yu : you might be the best person to answer this. Can someone tag him on Biostar?? Any help would be highly appreciated

[GenoMax]

You have already tagged Guangchuang in this post. Unfortunately he does not appear to have logged into Biostars for a month+.

Can you edit the title to make it concise?

Answer 1

[Guangchuang Yu]

This is an issue of re-root, you should ask the author of ape for the ape::root function.

[Chirag Parsania]

Hi Guangchuang,

Thanks for your reply. I didn't realise that root belongs ape. Anyway, I checked the documentation of ape::root. In fact after the critical review rerooting function of ape have been updated.