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?