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Description
Since hmmalign doesn’t fully align residues in insert columns, adding a parameter to automatically remove these columns could be a handy feature.
While hmmalign (in both PyHMMER and HMMER) already allows trimming of insert columns at the edges, my understanding is that HMMER doesn't offer an option to remove insert columns in the middle of the MSA because it would create "artificial" sequences. Nevertheless, I think this feature could be helpful since these columns aren't aligned anyway.
It’s not too difficult to remove them downstream, but I wanted to bring this up because I’ve recently seen several cases where unaligned columns were used for phylogenetic inference.