Where did profile-profile alignment go in v5? about muscle HOT 3 OPEN

Neither, really it's an oversight that profile-profile is not a command because it is a subroutine, Note that muscle v5 is not meant to be a replacement for muscle v3, it's a complete re-design which is complementary in some ways, e.g. there are datasets that muscle v3 can easily handle which are too big for muscle v5 (long sequences), and vice versa (many sequences). I'll leave this issue open as a feature request, hopefully I'll get to this before long, but probably not :-(

from muscle.

Different concept. Ensembles are alternative MSAs which are equally good, this allows you to test whether the inferences you are making from the alignments are robust.

For typical easy alignment problems, it doesn't matter which software you use -- clustal, mafft, muscle will all give very similar results. If the alignment is hard, then they will give different results, and the question is whether the differences matter in practice. This question is answered by making a muscle v5 ensemble, because the variants all have state-of-the-art accuracy.

from muscle.

Thanks for the swift response and yes, that was my impression more or less. Again, kudos on both designs (v3 and 5).

Given this state of things i don't see why i wouldn't just continue using 3.8. It works really well for me, but am wondering anyway if the profile-profile can be replicated more or less with the "ensembles" in v5 or it's a different concept?

from muscle.