Dear Sabrina.
What a great question.
The reason that you're seeing this behavior is because
prop.clades(rooted=TRUE) treats your trees as rooted; while
prop.clades(rooted=FALSE) treats them as unrooted.
The short answer to which you should use is that if your inference
method in the
Dear Ape team,
I am a researcher at the University of Cambridge (UK) and I had a quick
question regarding ape and creating boostrap trees.
I am struggling to understand the difference between prop.clades(root=FALSE)
and prop.clades(root=TRUE).
I am building ape trees based on methylation
