Closed ebraun68 closed 2 months ago
Thanks for asking, we should have documented it more clearly. This example command:
iqtree2 -s example.phy -m GTR+G -fast
will do the following steps (with comparison to a normal search when necessary):
Now your questions:
Q1. NNI is done both both starting trees, according to this workflow.
Q2. Stochasticity is only happening in step 2.
Q3. If you supply a starting tree via -t TREE_FILE
option: Step 2 is changed to using this tree and steps 4-5 won't do the NJ tree to keep the candidate set to have this one tree. The remaining steps stay the same.
I was curious about the -fast option. The only description I can find in the manual is this:
Turn on the fast tree search mode, where IQ-TREE will just construct two starting trees: maximum parsimony and BIONJ, which are then optimized by nearest neighbor interchange (NNI). Introduced in version 1.6.
I have a few questions about the details of this search:
1) Does IQ-TREE do NNIs on both starting trees, or does it check the likelihood of the MP and BIONJ trees and then choose one of those trees for further branch swapping?
2) How stochastic is this feature given different runs (or different random number seeds)? Is stochasticity coming in for the choice of MP starting tree, in the order of the NNIs, or both?
3) Can a -fast search be combined with a user starting tree?
I apologize if I missed any of this when I tried to find it in the manual