Rnaalifold

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