Sarah Lutteropp
Sarah Lutteropp
Still coming: - all_brlen_linkage_results - all_standard_random_results - all_standard_multi_results - (... likely some more) [all_prob_results.csv](https://github.com/lutteropp/NetRAX/files/6693483/all_prob_results.csv) [all_scaler_results.csv](https://github.com/lutteropp/NetRAX/files/6693485/all_scaler_results.csv) [all_unpartitioned_results.csv](https://github.com/lutteropp/NetRAX/files/6693486/all_unpartitioned_results.csv) [all_standard_results.csv](https://github.com/lutteropp/NetRAX/files/6693487/all_standard_results.csv)
We want to run NetRAX on this empirical dataset (from https://advances.sciencemag.org/content/5/5/eaav9188) which is available for download at https://bioweb.supagro.inra.fr/WheatRelativeHistory/index.php?menu=download - We need the IndividualAlignments data, which we merge together into one...
For all experiments, we will have (unless mentioned otherwise): - number of MSA sites = 1000 * (number of displayed trees) - perfect sampling: sites are sampled proportionally to the...
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...