Convert alignments into the exactness class efficiently

Construct efficient algorithms that convert a multiple sequence alignment with gaps into an alignment belonging to the class for which the gaps-as-symbols approach yields an optimal height-optimization solution, without sacrificing the original alignment score.

Background

Even if an input alignment does not belong to the class where treating gaps as symbols is exact, the paper asks whether it can be transformed into such an alignment. The unresolved requirement is that the transformation be efficient and preserve the alignment score.

References

Are there efficient algorithms to convert an MSA into one in this class without sacrificing the alignment score?

— Pangenome Optimization via Elastic Degenerate Strings  (2609.26542 - Rizzo et al., 22 Sep 2026) in Section Discussion, subsection “Gaps as symbols yield exact solutions?”