prot-msa

Multiple sequence alignment, conservation analysis, and position-specific mutation risk scoring. Uses mmseqs2/hhblits for real MSA when available, with ESM-2 pseudo-conservation as a zero-dependency fallback. Provides family-calibrated conservation scores, consensus sequences, coevolution signals, and low-risk mutation suggestions. Triggers whenever you need to assess how conserved a position is, build a consensus sequence, identify coevolving positions, or calibrate ESM-2 LLR with family context.