NetRAX Discussion of Experimental Results for "small_tree" (4-10 taxa, 0 reticulations)

The entire data (including the plots) is in here: https://drive.google.com/drive/folders/1odlBZo2LkJC9QitJMNJdxcVTgHIyDay1?usp=sharing

The experiments were done on my own laptop (LG Gram 17, 2019 model) using this commit version: https://github.com/lutteropp/NetRAX/commit/7bdd404edf5af335d5f0e441ec66c9ebcdae5913.

I decided against re-uploading each plot in this issue, as it made a messy message and did not provide any additional insight than the plots folder in the GoogleDrive link. Also, I am still adding new plots and improving the plots.

Dec 01 '20 10:12 lutteropp

Observations from this experiment:

NetRAX does similarly well as raxml-ng in inferring the correct tree.
On very few datasets, raxml-ng inferred one near-zero-branch in its ML tree.

Dec 01 '20 10:12 lutteropp

I agree with Sarah. Did we also inferred this near-zero-branch?

Dec 01 '20 11:12 celinescornavacca

Good question. I did not include this in the reported results file, but will check by hand by looking at the raw data (after asking Alexey what length is used as a threshold value to be a "near-zero" branch).

Dec 01 '20 11:12 lutteropp

Adding Alexeys Slack answer here for cross-reference:

it is "--blmin" which is 10^-6 by default:
https://github.com/amkozlov/raxml-ng/blob/master/src/main.cpp#L2201

Dec 01 '20 13:12 lutteropp