rnaconsensus

name	rnaconsensus
description	Use when predicting RNA secondary structures for single sequences using information from multiple sequence alignments of homologous sequences.
disable-model-invocation	true
user-invocable	true

rnaconsensus

Quick Start

• Command: RNAconsensus [-a filename] [-o OUTPUT] [--turn TURN] {hardcons,softcons} ...
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/RNAconsensus
• Full reference: See references/help.md for complete options and details

When To Use This Tool

• Predict single-sequence structures using consensus information from a homologous alignment.
• Map an RNAalifold consensus structure onto each sequence with hard constraints.
• Drive RNAfold -C-style per-sequence predictions from an alignment-derived consensus.
• Use the softer probabilistic strategy when hard constraints are too brittle.

Common Patterns

# 1) Produce hard constraints from an alignment plus RNAalifold output
RNAconsensus -a family.aln hardcons family.alifold > constraints.txt

# 2) Derive hard constraints from an RNAalifold dot plot
RNAconsensus -a family.aln hardcons -d alidot.ps -t 0.95 > constraints.txt

# 3) Run the soft-constraint strategy directly
RNAconsensus -a family.aln -o softcons.txt softcons

Recommended Workflow

1. Prepare a multiple sequence alignment file of homologous sequences
2. Choose a prediction strategy: hardcons (legacy refold.pl mode) or softcons (RNAsoftcons mode)
3. Run RNAconsensus -a <alignment_file> -o <output> <strategy>
4. Review output secondary structure predictions

Guardrails

• Requires a multiple sequence alignment file via -a flag
• Must specify either hardcons or softcons strategy
• Use --turn to set minimum hairpin length if needed
• --version is not implemented in this argparse wrapper even though --help works