rnalalifold

name	rnalalifold
description	Use when predicting locally stable secondary structures from multiple sequence alignments of RNA
disable-model-invocation	true
user-invocable	true

rnalalifold

Quick Start

• Command: RNALalifold [options] <file1.aln>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/RNALalifold
• Full reference: See references/help.md for complete options and details

When To Use This Tool

• Scan an RNA multiple sequence alignment for locally stable consensus structures.
• Find short structured elements inside long aligned regions instead of folding whole transcripts globally.
• Tune the maximum base-pair span for locality-sensitive searches.
• Export hit-specific alignments or CSV summaries for downstream review.

Common Patterns

# 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

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