Can I run mmseqs easy-cluster with gapped sequences?

[JinyuanSun]

I would like to cluster sequences with gaps, can I use mmseqs linclust or easy-cluster? Will the gaps in input sequences affect the identity calculation?

[milot-mirdita]

Do you mean the input sequences already have gaps? In this case, all non-amino-acid characters will get turned into the unknown residue X. So the sequences would get longer and it would affect sequence identity.