Behavior of --alt-ali in TM mode

[yonatan212]

Hello,

I have a question about the behavior of Foldseek when using the --alt-ali mode and TM-align for multiple iterations on the same protein.

When running a single search, I understand that there is an initial seed alignment, which expands using TM-align to achieve the final alignment. Is this correct?
In subsequent iterations (when searching multiple times within the same protein), what happens if the initial seed alignment is no longer available? How does the algorithm proceed to grow or refine the alignment without a seed?
I would greatly appreciate clarification on how the alignment process works in this scenario.

Thank you for your excellent work on Foldseek!

[milot-mirdita]

Currently, --alt-ali doesn't really work in combination with the tmalign mode. We should disable setting both at the same time.

This sounds like a useful feature for the future though