MMseqs2 vs jackhmmer - performance difference

[divnori]

Thank you for the code release!

I have a question about performance using precomputed MSAs (with MMseqs2) vs on-the-fly MSA computation with jackhmmer. I am comparing performance between (i) passing in precomputed unpaired MSAs from colabfold both with and without template search (no paired MSA) and (ii) letting AF3 compute everything (unpaired MSA, paired MSA, templates).

While the results look similar upon visual inspection, I am seeing much higher ipTM and ranking scores with jackhmmer. Is this expected? Have others observed a similar effect? I see some discussion about this in a previous issue but not sure whether people have further information now.

Appreciate your help - thanks.