Layouts
Circular
Circular layouts are mainly used (1) if the displayed sequence itself is circular, (2) to display a non-circular sequence in a space-saving way, and (3) to show interactions between different parts of the sequence(s) using a chord diagram.
17 tools
Linear
Linear layouts are more intuitive and easy to read, but may be extremely long and require zooming and panning.
95 tools
ABrowse
AliView
Alvis
Apollo
BactoGenie
BedSect
CEpBrowser
Cinteny
CNVkit
Combo
Cooler
CRAMER
CRISPResso2
Dalliance
Deep Motif Dashboard
deepTools Heatmap
DNAPlotter
EaSeq
Edgar Genome Browser
Edgar Synteny Plots
EnrichedHeatmap
Ensembl
EpiViz
Galaxy HiCExplorer
GBrowse
GBrowse_syn
Geneious
Genome Annotator Light (GAL)
GenomeView
genoPlotR
GenPlay
Gepard
ggBio
GIVE
Gosling
Gremlin
GView
HiGlass
HiPiler
HUGIn
IGB
Integrative Genomics Viewer
IRScope
Island Viewer
JalView
JBrowse
JuiceBox
Juiceboxjs
Lollipop Plot cBio
MAGI
MEME
MEXPRESS
MGcV
MicroScope
MizBee
MochiView
MSAViewer
my5c
NCBI Genome Viewer
NCBI Sequence Viewer
ngs.plot
Oviz-Bio
Persephone
pLogo
PSU 3D Genome Browser
ReadXplorer
RIdeogram
Sashimi Plot
Savant Genome Browser 2
SCGV
Sequence Bundles
Sequence Surveyor
SilkDB 3.0
Spatial DB
SpliceGrapher
SplicePlot
SpliceSeq
svist4get
SWAV
SynMap2
SynteBase and SynteView
Synteny Explorer
TFmotifView
trackViewer
Two Sample Logo
UCSC Genome Browser
Variant View
VCF Plotein
Vials
Vista Dot
Vista Synteny
VistaPoint
WashU Epigenome Browser
WebLogo
Xena
Space Filling
The space-filling curve is more space efficient than a circular layout and is often used to display a global overview of the genome while maintaining the spatial distribution of features. However, space-filling curves can only show one feature set, and it's hard to visually estimate the distances between two positions in a sequence.
2 tools
Spatial
Spatial layouts display sequences in a 3-dimensional structure.
2 tools