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 bootstrapping analysis estimates an unrooted tree, you
should set prop.clades(rooted=FALSE). *Most* phylogeny inference methods
(ML, MP, NJ, ME, LS) estimate *unrooted* trees; only UPGMA and molecular
clock methods estimate rooted trees.
All the best, Liam
Liam J. Revell
University of Massachusetts Boston
Universidad Católica de la Ssma Concepción
web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org
Academic Director UMass Boston Chile Abroad:
https://www.umb.edu/academics/caps/international/biology_chile
On 9/18/2020 7:52 AM, Sabrina Rossi wrote:
[EXTERNAL SENDER]
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 data for kidney cancer tissue.
When I use boot.phylo (1000 bootstraps) and prop.clades with unrooted trees,
the output of prop.clades is 100% for all the clades. In other words, the
clades return the same result for all 1000 bootstrap trees.
However, when the same thing is repeated with a rooted tree of the same data,
the output of prop.clades is very different: 100% 18% 30% 35% 73% 81% 62%
70% 77% 84%. In other words, the clades are very different for the bootstrap
trees.
Would you please be able to help me understand the difference between
prop.clades with root=TRUE versus root=FALSE?
Or do you have any useful reading material that may explain this? I cannot find
anything on the internet.
What is the best practice, rooted or unrooted, considering I get completely
different results?
Thank you very much for taking the time to answer my question
Best wishes
Dr Sabrina Rossi
BSc MPhil MBChB MRCS
University of Cambridge
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