rnaalifold

name	rnaalifold
description	Use when predicting consensus secondary structures from multiple sequence alignments of RNA. Computes minimum free energy structures, partition functions, and base pairing probabilities for aligned RNA sequences.
disable-model-invocation	true
user-invocable	true

rnaalifold

Quick Start

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

When To Use This Tool

• Predict a consensus secondary structure from an RNA multiple sequence alignment.
• Add ensemble probabilities with -p instead of relying on MFE alone.
• Quantify structural conservation with --sci.
• Generate alignment-wide structure and dot-plot outputs from one run.

Common Patterns

# 1) Predict the consensus MFE structure from an alignment
RNAalifold family.aln

# 2) Add partition function and pairing probabilities
RNAalifold -p family.aln

# 3) Compute SCI for a conserved alignment
RNAalifold -p --sci family.aln > alifold.txt

Recommended Workflow

1. Prepare input alignment in CLUSTAL, Stockholm, FASTA, or MAF format
2. Run basic consensus prediction: RNAalifold alignment.aln
3. Add partition function for probabilities: RNAalifold -p alignment.aln
4. Review output files: alirna.ps (structure), alidot.ps (dot plot), alifold.out (credibility-sorted pair list)

Guardrails

• Input must be a valid multiple sequence alignment in CLUSTAL, Stockholm, FASTA, or MAF format
• Avoid mixing very similar and dissimilar sequences; duplicate sequences can distort predictions
• Output files overwrite existing files of the same name in the current directory