rnapdist

name	rnapdist
description	Use when calculating structure distances between thermodynamic ensembles of RNA secondary structures from sequence input.
disable-model-invocation	true
user-invocable	true

rnapdist

Quick Start

• Command: RNApdist [OPTION]... — reads RNA sequences from stdin
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/RNApdist
• Full reference: See references/help.md for all options and details

When To Use This Tool

• Use RNApdist when you need to compare RNA sequences by the distance between their thermodynamic structure ensembles, not by sequence identity alone.
• It is useful for asking whether two RNAs have similar folding landscapes even if their minimum-free-energy structures are not identical.
• Switch comparison mode with -X when you need a specific ensemble-distance definition for your analysis.
• Use -B when you want a profile-style alignment output in addition to the distance values.

Common Patterns

# Compare two or more sequences from stdin using the default profile distance
printf 'GGGAAAUCC\nGGAAAUUCC\n' | RNApdist

# Use an alternative comparison directive
printf 'GGGAAAUCC\nGGAAAUUCC\n' | RNApdist -X m

# Emit a backtracked profile alignment to a file
printf 'GGGAAAUCC\nGGAAAUUCC\n' | RNApdist -B profiles.txt

# Recompute ensemble distances at a different temperature
printf 'GGGAAAUCC\nGGAAAUUCC\n' | RNApdist -T 25

Recommended Workflow

1. Prepare input RNA sequences (FASTA or plain format) for comparison
2. Select comparison mode with -X (p, m, f, or c; default is p)
3. Run RNApdist with appropriate options (e.g., -T for temperature, --salt for salt concentration)
4. Review distance output; optionally use -B to generate aligned structure profiles

Guardrails

• Input is read from stdin; ensure sequences are provided via pipe or redirect
• Default temperature is 37°C and salt concentration is 1.021M; adjust with -T and --salt if needed
• Nucleotide "T" is automatically converted to "U" unless --noconv is specified