Comparing unequal trees

Question

[Joe]

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?

Answer 1

[Joseph Hughes]

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.

[Joe]

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?

[Joseph Hughes]

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