Sarah Lutteropp

I am resubmitting **all** the experiments from this issue with 15 taxa now. We now can use all threads on a cluster node in NetRAX (with disabled site repeats, thanks...

Switching to another server that has no time limit doesn't help with: - 3 reticulations on a 10-taxon-nonweird network being impossible - Some potential bugs or endless loops (e.g., in...

I figured out a problem: The new experiment script had a bug in change reticulation probs -> it overwrote the network file with a tree That's why I kept inferring...

(Copy&paste from Slack message) I redid the simulation experiments and changed the experimental settings. The old ones appeared useless to me. The new experimental setting is: - Always start from...

Regarding evaluation of Likelihoodmodel.BEST vs. LikelihoodModel.AVERAGE: If we want to do this properly, then we need to scramble partitions and somewhat randomly assign sites from different displayed trees to a...

The problem with starting the network search from multiple random/parsimony trees is: - For low number of taxa, it is unlikely that raxml-ng best tree is a bad starting choice....

>I don't get what brlen scaler means here and how you can just set it to those values. It was some old experiment where we scaled the branches of the...

The raxml-ng best-tree based network inference was not always the one getting the best network in the end. But the differences were minimal. And the underlying problem is that we...

>in reality we don't know the branch model, hence knowing what the impact of using the wrong one is, is interesting. Ok, I will also run some inferences with the...

Regarding unlinked branches, we already had some past discussions with @celinescornavacca discussing that they are incapable of inferring some reticulations. See https://github.com/lutteropp/NetRAX/issues/33 Also, @stamatak said here that only using linked...