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 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?
It is written several files when finalizing the analysis, is there someone more appropriate to check bs support under this '-Q partitions' scheme?
Thank you all,