Question: Statistically defining deep branching clades in phylogenetic tree
gravatar for Daniel
17 months ago by
Cardiff University
Daniel3.8k wrote:

I have a phylogenetic tree which visually has 3 major clades, one of which forks into two minor clades. I am discussing the groups in the text in regards to the metadata but I want to statistically/technically describe why the groups are seperate.

What is the best way to achieve this? The tree is UPGMA Jackknife generated, with around 150 samples. Note: These are not based on sequence similarity but community structure, so it has to be based on the tree rather than that underlying sequence or similar.

I have been looking at and the package but can't see a way to achieve this.


trees phylogenetics • 363 views
ADD COMMENTlink written 17 months ago by Daniel3.8k

I’ve used Simon Harris’ script ( to ‘objectively define clades’ in the past to varying degrees of success. May be of interest?

ADD REPLYlink written 17 months ago by Joe15k

Thanks for the suggestion. I've been giving it a go but it's basically only identifying everything into one cluster. Having a look at ete but not solved it yet.

ADD REPLYlink written 17 months ago by Daniel3.8k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1632 users visited in the last hour