Question: Comparing unequal trees
gravatar for Joe
3.0 years ago by
United Kingdom
Joe15k wrote:

On some of the suggestions here: A: Metrics to evaluate tree congruence

I'm taking a look at the ete3 toolkit and others, but I have a question:

When comparing congruency with robinson-foulds, are branch lengths taken in to consideration?

I have a number of gene trees which each have branch lengths as they're computed from alignments as usual. From these I used ASTRAL to infer a species tree however, which does not (and as far as I'm aware cannot) have branch lengths.

If I compare these for congruency, will I get a misleading answer as there's no branch length in the reference species tree?

trees phylogenetics • 852 views
ADD COMMENTlink modified 3.0 years ago by Joseph Hughes2.8k • written 3.0 years ago by Joe15k
gravatar for Joseph Hughes
3.0 years ago by
Joseph Hughes2.8k
Scotland, UK
Joseph Hughes2.8k wrote:

The robinson-foulds counts the number of operations that are needed to transform one tree topology into another and this measure is the RF distance. The branch lengths of the tree are not taken into account.

ADD COMMENTlink written 3.0 years ago by Joseph Hughes2.8k

Perfect, that's all I needed to know! Though as a follow up, are there congruency methods where branch lengths do matter? Perhaps in the corphenetic coefficient mentioned in the linked thread for example?

ADD REPLYlink written 3.0 years ago by Joe15k

There are measures like the Branch Length distance by Kuhner and Felsenstein (1994) and measures like the K tree score. And probably others.

ADD REPLYlink written 3.0 years ago by Joseph Hughes2.8k
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