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 [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylo&data=02%7C01%7Cliam.revell%40umb.edu%7C642a8093de024d4c45f908d85c1a1304%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637360614343423569&sdata=1lPGmceyxBAlmgaT8UECbAgzu2DxYI%2F2RZePh9uSFfA%3D&reserved=0 Searchable archive at https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2F&data=02%7C01%7Cliam.revell%40umb.edu%7C642a8093de024d4c45f908d85c1a1304%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637360614343423569&sdata=7uL82jhBPH9alEUYdg0xGXTDQRXcluopc3Luf77zwSE%3D&reserved=0
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