Rnalalifold

# 2) Tighten the local window size
RNALalifold -L 100 family.aln

# 3) Emit CSV plus per-hit alignment outputs
RNALalifold --csv --aln hits family.aln > local_hits.txt

Recommended Workflow

1. Prepare input as a multiple sequence alignment file (MSA) in supported format
2. Set maximum base pair span with -L if different from default 70
3. Run RNALalifold with appropriate options (e.g., --threshold, --csv, --aln for output)
4. Review output consensus structures and energy values per hit

Guardrails

• Input must be an aligned RNA sequence file (MSA); verify format matches -f option if specified
• Memory usage scales as O(n+LL) and CPU time as O(nL*L) where L is maxBPspan
• Default threshold of -0.1 kcal/mol per nucleotide filters weak structure hits; adjust with --threshold if needed