rnaaliduplex

name	rnaaliduplex
description	Use when predicting conserved RNA-RNA interactions between two CLUSTAL alignments to identify evolutionary conserved binding sites, hybridization energies, and duplex structures.
disable-model-invocation	true
user-invocable	true

rnaaliduplex

Quick Start

• Command: RNAaliduplex [options] <file1.aln> <file2.aln>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/RNAaliduplex
• Full reference: See references/help.md for complete options and details

When To Use This Tool

• Predict conserved RNA-RNA interactions between two homologous alignments.
• Score duplexes while preserving evolutionary signal across matched sequence sets.
• Search for optimal and suboptimal binding sites between a probe alignment and a target alignment.
• Keep analysis focused on inter-molecular pairing only.

Common Patterns

# 1) Predict the best conserved interaction between two alignments
RNAaliduplex probe.aln target.aln

# 2) Report suboptimal interactions within an energy band
RNAaliduplex -e 5 probe.aln target.aln