rnaforester

name	rnaforester
description	Use when comparing, aligning, or computing similarity/distance between RNA secondary structures, or when generating multiple structure alignments with consensus prediction.
disable-model-invocation	true
user-invocable	true

rnaforester

Quick Start

• Command: RNAforester [options]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/RNAforester
• Full reference: See references/help.md for complete options and usage details

When To Use This Tool

• Align or score RNA secondary structures directly rather than folding sequences anew.
• Run local, global, or small-in-large structure comparisons.
• Build multiple structure alignments with consensus prediction.
• Generate 2D alignment plots for manual inspection.

Common Patterns

# 1) Align structures from an input file
RNAforester -f=structures.txt

# 2) Compute local structural similarity
RNAforester -l -f=structures.txt

# 3) Predict structures from sequences before aligning them
RNAforester -p -f=sequences.fa > forester.out

Recommended Workflow

1. Prepare input structures in file and verify format compatibility
2. Run RNAforester -f=inputfile for basic structure alignment, or add -l for local similarity, -s for small-in-large, or -m for multiple alignment mode
3. Use -p to predict structures from sequences when needed, or --score to compute only scores without alignment output
4. Generate visualization with -2d for PostScript 2D plots if alignment inspection is needed

Guardrails

• Input files require valid RNA secondary structure format; verify structure syntax before running
• Scoring parameters (-pm, -pd, -bm, -br, etc.) significantly affect results—use defaults unless specific tuning is required
• For multiple alignment mode (-m), consider clustering thresholds (-mt, -mc) to control alignment granularity