Use when predicting locally stable secondary structures from multiple sequence alignments of RNA
RNALalifold [options] <file1.aln>/home/vimalinx/miniforge3/envs/bio/bin/RNALalifold# 1) Scan an alignment for local consensus structures
RNALalifold family.aln
# 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
-L if different from default 70RNALalifold with appropriate options (e.g., --threshold, --csv, --aln for output)-f option if specified--threshold if needed