Does -Q inflate bootstrap support, or is it 'reliable'? (v. >2)

[tunasdelsur]

Dear all,

I recently concatenated hundreds of nuclear loci (~500), and I ran iqtree using

iqtree2 -s myalignment.fasta -Q partitions.txt -T AUTO -m TEST -B 5000

and apparently got 100bs values for all my relationships - which is not concordant with my previous Astral species tree, nor with a preliminary iqtree ran missing "-Q partitions.txt". How does that argument is working on my data? I know bootstraps are super estimated when we know that some datasets can have a lot of gene tree discordances on some backbone topologies and still get 100 bs values, but is this value from -Q reliable? On the .log file, it is written the following files (below), is there some more appropriate to check bs support? Thank you all.

Analysis results written to:
IQ-TREE report: partitions.txt.iqtree
Maximum-likelihood tree: partitions.txt.treefile
Partition trees: partitions.txt.parttrees
Likelihood distances: partitions.txt.mldist
Best partitioning scheme: partitions.txt.best_scheme.nex
in RAxML format: partitions.txt.best_scheme

Ultrafast bootstrap approximation results written to:
Split support values: partitions.txt.splits.nex
Consensus tree: partitions.txt.contree
Screen log file: partitions.txt.log