Sarah Lutteropp

I believe it is *not* a problem, because with relative RF-distance it is kinda the same issue...

Do we need to exclude the trivial bipartitions/clusters when computing the network distances? I tried finding the definition for relative RF distance to check how it is done there, but...

Thanks @stamatak! So we need to diverge from the distance definitions in Celines network book: We will explicitly discard the trivial bipartitions/clusters/whatever in our own distance implementations.

How about these two experimental setups: A: Start NetRAX from 10 random + 10 parsimony trees B: Start NetRAX from only the best RAxML-tree

I implemented the two setups I suggested above. Let's see how it behaves in our experiments now! :)

Turns out 10 random + 10 parsimony trees are a bit much... especially since the current NetRAX version is only single-threaded and not optimized for runtime performance yet (it wastes...

If we don't care aabout runtime at all: Should I also switch to the slower network search algorithm? So far, I accepted the first move that improved the BIC score....

With the new wavesearch algorithm, I do not see any advantage in starting from multiple starting trees vs. starting from best raxml-ng tree.

In LikelihoodModel.AVERAGE, the negative influence comes from the reticulation probabilities being always linked among all partitions. We would not have a negative influence here if each partition would have its...

Cool! Then we can do all experiments in LINKED mode! :-) This one also performed best in the anecdotal experience I had so far. I believe (from reading the simulator...