rnadistance

name	rnadistance
description	Use when calculating distances between RNA secondary structures, including base pair distance and tree or string editing-based dissimilarity measures.
disable-model-invocation	true
user-invocable	true

rnadistance

Quick Start

• Command: RNAdistance [OPTION]...
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/RNAdistance
• Full reference: See references/help.md for complete options

When To Use This Tool

• Quantify how different two RNA secondary structures are.
• Compare structures with base-pair distance or tree/string-edit representations.
• Switch to Shapiro's coarse-grained cost matrix with -S when you care about abstract motifs.
• Emit aligned backtracks to inspect which substructures match.

Common Patterns

# 1) Compute default distances between two structures from stdin
printf '(((...)))\n((.....))\n' | RNAdistance

# 2) Choose a specific distance representation
printf '(((...)))\n((.....))\n' | RNAdistance -D f -X p

# 3) Write an aligned backtrack to a file
printf '(((...)))\n((.....))\n' | RNAdistance -B=alignment.txt

Recommended Workflow

1. Prepare RNA secondary structure inputs to compare
2. Select distance representation with -D (default f) and comparison directive with -X (default p)
3. Run RNAdistance with structures via stdin, optionally enabling -S for Shapiro's cost matrix or -B for backtrack output
4. Interpret distance values; use backtracking output to visualize structural matches

Guardrails

• Do not use base pair distance for structures of different lengths (not recommended per documentation)
• Provide RNA secondary structures via stdin before invoking
• Specify output filename with -B=<filename> if alignment/backtrack output is needed