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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