rnaplot

name	rnaplot
description	Use when visualizing RNA secondary structures from dot-bracket notation or Stockholm alignments, generating structure diagrams, or creating annotated consensus structure plots.
disable-model-invocation	true
user-invocable	true

rnaplot

Quick Start

• Command: RNAplot
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/RNAplot
• Full reference: See references/help.md for detailed options

When To Use This Tool

• Render RNA secondary structures from RNAfold-style sequence/structure input.
• Convert one structure drawing into EPS, SVG, GML, XRNA, or SSV output.
• Plot consensus structures from Stockholm alignments.
• Add covariance or alignment annotation for comparative displays.

Common Patterns

# 1) Draw a structure from an RNAfold-style input file
RNAplot -i fold.txt

# 2) Switch the output format to SVG
RNAplot -i fold.txt -f svg

# 3) Plot a consensus structure from an alignment with covariance annotation
RNAplot -a --covar --aln -i family.stk

Recommended Workflow

1. Prepare input in RNAfold output format or Stockholm 1.0 alignment format with secondary structure
2. Run RNAplot -i <input_file> for basic structure visualization
3. Specify output format with -f option (eps, svg, gml, xrna, ssv) if non-default needed
4. Adjust layout algorithm with --layout-type (0-4) or add covariance annotation with --covar for consensus structures

Guardrails

• Input must include secondary structure notation (not just sequences)
• Existing output files of the same name will be overwritten without warning
• Use -a flag when providing Stockholm format multiple sequence alignments