How to root a tree after importing with read.raxml()

[Todd Knutson]

Hi, I am having trouble re-rooting a tree that has been imported via the read.raxml() function. I am reading in the "RAxML_bipartitionsBranchLabels.H3" file from RAxML. 

How can I re-root (or midpoint root) this tree? I want the bootstrap values to remain accurate after rooting. I have been trying to use the following method:

library(phangorn)

bi_BL_raxml_tree_midroot@phylo <- midpoint(bi_BL_raxml_tree_midroot@phylo)

or

bi_BL_raxml_tree_rooted@phylo <- reroot(bi_BL_raxml_tree_rooted@phylo, 79)

But I think this changes the node and bootstrap labels -- making them incorrect. Any help rooting a raxml object would be very helpful.

Thanks

[biliang zhang]

Here is the solution.

https://github.com/GuangchuangYu/ggtree/issues/15


在 2016年11月10日星期四 UTC+8上午10:44:29，Todd Knutson写道：