Dear Colleagues,
Do you know some more or less formalized method(s) to compare topology etc. of two different taxa and some other characters of trees (not tanglegram = congruence of terminal clades). The same for haplotype networks. Question - we have 10 different networks for 10 taxa. Which two of them are most similar I e. in topology... ?
With best wishes
Alexey
In any case there should be few common taxa. Any comparative method will address this overlapping part. I have used 2 methods: one is quartet-based. There are only 3 different topologies of a 4-leaves tree, thus one may count the ratio of similar quartets. Average ration or occasionally coinciding quartets is 1/3. If you have more, the trees are similar in the overlapping part. The other (seemingly more common) is based on phyletic distances between OTUs and is implemented in Python library ete3 (http://etetoolkit.org). Caution there: there is some format incompatibility in tree-drawing part on a linux/python-3.10 box. Hope they will fix it!
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