rnaeval

name	rnaeval
description	Use when evaluating the free energy (kcal/mol) of an RNA secondary structure, calculating co-folding energies for two RNA strands, or analyzing consensus structures from multiple sequence alignments.
disable-model-invocation	true
user-invocable	true

rnaeval

Quick Start

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

When To Use This Tool

• Use RNAeval when you already have a sequence plus a proposed dot-bracket structure and want its free energy scored.
• It is the right tool for rescoring externally generated structures, checking cofold energies for two strands separated by &, or auditing loop-by-loop contributions with -v.
• Use --msa when the input is a Stockholm multiple-sequence alignment plus a consensus structure.
• Do not use it to predict structures from sequence alone; this program evaluates a supplied structure rather than searching for one.

Common Patterns

# Evaluate one sequence/structure pair from stdin
printf 'GGGAAAUCC\n(((...)))\n@\n' | RNAeval

# Print detailed loop-energy contributions
printf 'GGGAAAUCC\n(((...)))\n@\n' | RNAeval -v

# Evaluate a two-strand cofold structure marked with &
printf 'GGGA&AAAUCC\n(((.&.)))\n@\n' | RNAeval

# Read sequence/structure input from a file
RNAeval -i structures.txt

Recommended Workflow

1. Prepare input with RNA sequence and dot-bracket structure (one per line or in file)
2. Run RNAeval -i <inputfile> or pipe input via stdin
3. Review energy output in kcal/mol; use -v for per-loop breakdown if needed
4. For alignments, use --msa with Stockholm 1.0 format input

Guardrails

• Input must include both sequence and structure; this tool does not predict structures
• End batch input with a line containing only @ or ensure proper EOF handling
• Ensure sequences use U not T (or use --noconv to disable auto-conversion)