Sarah Lutteropp

Thanks for the reminder! For networks, this part should be simple. The network root never changes. During brlen optimization, we only evaluate the displayed trees at some other node tempRoot...

I need to redo some evaluation parts - the computation of true network weirdness currently always reports 0.0 (see https://github.com/lutteropp/NetRAX/issues/44)

I've checked the pll-modules source code for logl computation during brlen optimization. If I got it correctly, then: - During optimization of a branch, we don't need to recompute any...

> A pretty counter-intuitive observation: Not sure if it's statistically significant, but it looks like having a MSA size of (number of displayed trees) * 100 leads to slightly **worse**...

I need to double-check how one computes the changed displayed tree loglikelihood after a branch length has been changed during the brlen opt. Am I using the right CLVs? Is...

Maybe I need pll_compute_root_loglikelihood instead of pll_compute_edge_loglikelihood?

No that can't be, pll_compute_edge_loglikelihood sounds about right... maybe drawing a picture helps

 I have this zero-reticulation rooted network. I want to optimize the branch with pmatrix index 27, which is highlighted in green in the picture. The edge...

 I asked Alexey how a CLV knows the rest of the tree (the parts not below it) and Alexey figured out the problem: When the virtual root of a...

The affected CLVs are exactly the ones on the path from the temporary virtual root to the network root. Thus, one not only needs to invalidate them after the branch...