NetRAX
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lutteropp
Phylogenetic Network Inference without ILS
CLV of a node ->Weighted average of CLVs from different cases. See picture. 
Nearly all of the runtime (> 90%) now gets spent in ranking move candidates. This is because we currently rank move candidates based on the BIC score we get after...
(from https://github.com/lutteropp/NetRAX/issues/43) > Use Newton-Raphson instead of Brent for optimizing branches (this will give us some niiiiiice additional speedup). This requires some Maths now, as I need to understand how...
Currently, branch length optimization is where most of the NetRAX runtime is spent. I was wondering: If we change a single branch length, do we need to care about loglikelihood...
Naively, one would store `number_of_network_nodes * number_of_displayed_trees` CLV vectors. However, there are regions in the network that are exactly the same over multiple displayed trees. Those regions can be identified...
Why do trees with (unrooted) RF-distance of zero have non-zero Dendroscope distances? Does it have to do with the rooting somehow? See screenshot from a results.csv file, used (in different...
@celinescornavacca I've read the part in your book about hardwired/softwired clusters in rooted phylogenetic networks. Now I understand what these are: - A _cluster_ induced by an edge is the...
How is the ancestral state defined in networks? If we have the ancestral states for all displayed trees, how do we get the ancestral states for the network? Is it...
The completed results CSV files from the cluster experiments are finally there. - small_network: 4-10 taxa, 1-2 reticulations, msa-size either 100*n_trees or 200*n_trees, perfect sampling, linked branches, both likelihood variants,...
With the current horizontal rNNI and rSPR moves, can we place a reticulation somewhere else **in a single step**? I think no... It looks to me that we can only...