0.16.6 documentation

Site guide · find your task

Setup and learning paths

HomeInstall and prepare the environmentChoose your learning module

Module I · Chord

1.1 Tables and field meanings1.2 Produce and import comparisons1.3 Build the layers step by step1.4 Direction, curvature and clearance1.5 Filter and summarize links1.6 Full source-file workflow1.7 Complete chord showcase

Module II · Collinear

2.1 Reuse chord input tables2.2 Switch coordinates and add layers2.3 Routes, clearance and the ruler2.4 Compare CDS neighbourhoods2.5 Focus, anchors and segments2.6 Complete collinear showcase

Module III · Plasmid

3.1 DNA, annotations and 13 references3.2 From a circle to annotation layers3.3 Features, primers and restriction3.4 Thirteen plasmid references3.5 Complete plasmid cases

Consult as needed · Data and layers

Prepare tables and coordinatesImport and convert dataImport nucleotide and protein alignmentsProject protein intervals to genomic coordinatesFeatures, stacking and genomic decorationLabels and local placementQuantitative tracksMappings, scales, guides and themesSet values by sequence and strandCommon adjustments and grammarExport, preview and diagnostics

Learning map and reference

Articles and complete workflowsFunction referenceReproducible galleryFrequently asked questionsMigrate to the candidate APITerminology and design sourcesDevelopment status and changes

Articles and complete workflows

On this page

• Three learning paths
• Read in order or consult as needed
• Setup and learning paths
• Module I · Chord
• Module II · Collinear
• Module III · Plasmid
• Consult as needed · Data and layers
• Learning map and reference
• Capabilities and runnable evidence

Learn progressively inside a module, then consult shared techniques as needed. Each path starts with tables and ends with a complete showcase.

Three learning paths

Module I · ChordTables → import → backbones and layers → geometry and clearance → showcase Module II · CollinearReuse inputs → replace coordinates → route long links → local comparisons → showcase Module III · PlasmidDNA and annotations → circle and layers → recognition → 13 cases → dense showcase

Read in order or consult as needed

Setup and learning paths

• Install and prepare the environment
• Choose your learning module

Module I · Chord

• 1.1 Tables and field meanings
• 1.2 Produce and import comparisons
• 1.3 Build the layers step by step
• 1.4 Direction, curvature and clearance
• 1.5 Filter and summarize links
• 1.6 Full source-file workflow
• 1.7 Complete chord showcase

Module II · Collinear

• 2.1 Reuse chord input tables
• 2.2 Switch coordinates and add layers
• 2.3 Routes, clearance and the ruler
• 2.4 Compare CDS neighbourhoods
• 2.5 Focus, anchors and segments
• 2.6 Complete collinear showcase

Module III · Plasmid

• 3.1 DNA, annotations and 13 references
• 3.2 From a circle to annotation layers
• 3.3 Features, primers and restriction
• 3.4 Thirteen plasmid references
• 3.5 Complete plasmid cases

Consult as needed · Data and layers

• Prepare tables and coordinates
• Import and convert data
• Import nucleotide and protein alignments
• Project protein intervals to genomic coordinates
• Features, stacking and genomic decoration
• Labels and local placement
• Quantitative tracks
• Mappings, scales, guides and themes
• Set values by sequence and strand
• Common adjustments and grammar
• Export, preview and diagnostics

Learning map and reference

• Reproducible gallery
• Frequently asked questions
• Migrate to the candidate API
• Terminology and design sources

Capabilities and runnable evidence

Capability	Read	Executable source / output
Three coordinate modes	Choose your learning module	chord, circular, collinear · chord, circular, collinear
Original-record comparisons	1.6 Full source-file workflow	realimport, realprepare, realchord, reallinear · realchord, reallinear
Complete circular annotation	3.5 Complete plasmid cases	plasmid · plasmid
Validation, cleaning and hierarchy	Prepare tables and coordinates	validation, cleaning, hierarchy
Formats and adapters	Import and convert data, Import nucleotide and protein alignments	adapters, formats, genbank, optionalranges, standardblast, protein · paf
Link preparation and statistics	1.5 Filter and summarize links	ribbons · density
Interval and point links	1.5 Filter and summarize links, Choose your learning module	pointlinks, collinear · pointlinks
Features and Position	Features, stacking and genomic decoration	featurestack · featurestack
Automatic and fixed labels	Labels and local placement, 3.5 Complete plasmid cases	labellayouts, labels, plasmid · labelauto, labelradial, labelarc
Axes, scale bars and regions	Features, stacking and genomic decoration, 2.5 Focus, anchors and segments	decorations, focus · decorations
Quantitative tracks and domains	Quantitative tracks	tracks, multitrack · multitrack
Primers, sites and feature search	3.3 Features, primers and restriction, 3.5 Complete plasmid cases	recognition, plasmid · plasmid
CDS and link projection	Project protein intervals to genomic coordinates, 2.4 Compare CDS neighbourhoods	projection, linkprojection
Explicit clusters and loci	2.4 Compare CDS neighbourhoods	homologs · homologs
Focus, segments and source mapping	2.5 Focus, anchors and segments	focus, segment, mappingposition · focus
Scales, guides and themes	Mappings, scales, guides and themes, Common adjustments and grammar, Set values by sequence and strand	styling, adjustments, parameters · styling
Preview, results and ordering	Export, preview and diagnostics	save, preview, provenance, layoutresults
Migration and FAQ	Migrate to the candidate API, Frequently asked questions	migration