Visualisation Tools

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This is a collection of many of the most notable visualisation tools produced by biologists and visualisation researchers. If you have a tool you would like to see here, please register and you will be able to add your visualisation tool to the site or contact us for more advice.

HiGlass showing several ChIP-seq tracks with a Hi-C map
HiGlass
Genome
Scalable Insets
Genome
karyoploteR
Genome
BioBlox
Molecular
SATORI's interface
SATORI
Genome
HiPiler's interface
HiPiler
Genome
MLCut
MLCut
Genome
SeqMonk
Genome
HaptiMOL
HaptiMOL
Molecular
Reactome
Pathway
xiNET
xiNET
Molecular
OneZoom - mammals
OneZoom
Phylogenetics
FigTree
FigTree
Phylogenetics
Epiviz
Epiviz
Genome
VisRseq
Genome
expVIP
expVIP
Genome
gene.iobio.io
iobio
Genome
Aquaria
Aquaria
Molecular
EK3D logo
EK3D
Genome
Annotools overview
Annotools
Genome
Phandango - metadata example
Phandango
Genome, Phylogenetics
NinjaViewer interface
NinjaViewer
Genome
Gene Expression Commons - geneset activity profiling
Gene Expression Commons
Genome
RCSB PDB logo
RCSB Protein Data Bank
Molecular
GenomeCRISPR concept
GenomeCRISPR
Genome
Hi-C Explorer
Genome
cellVIEW
Molecular
Mango interface
Mango
Genome
ClearVolume
SynTView
Genome
PlantGenIE
Genome
MegaMol
Molecular
CooccurViewer
Cells and Organisms, Genome
Pan-Tetris
Genome
Molecular Maya molecular modeling simulation intuitive
Molecular Maya
Molecular
Integrated Genome Browser
Integrated Genome Browser
Genome
GraphiteLifeExplorer
GraphiteLifeExplorer
Molecular
OMERO
Sequence logo viewer
Genome
Aequatus
Genome
TGAC Browser
Genome
SequenceJuxtaposer
SequenceJuxtaposer
Genome
Pipit
Pipit
Genome
Zomit
Zomit
Genome
ArkMAP
ArkMAP
Genome
GenotypeChecker
GenotypeChecker
Genome, Populations
TaxonTree
TaxonTree
Phylogenetics
TJ sunflower pictures. TreeJuxtaposer
TreeJuxtaposer
Phylogenetics
BioFabric
BioFabric
Pathway
PhyloDet
PhyloDet
Phylogenetics
Dendroscope
Dendroscope
Phylogenetics
Variant View
Variant View
Genome
Strudel
Strudel
Genome
HerbariaViz
HerbariaViz
Populations
Silva Tree Viewer screenshot
Silva Tree Viewer
Cells and Organisms, Phylogenetics
Pseudoviewer
Pseudoviewer 3
Genome, Molecular
IGV
IGV
Genome
TCA cycle showing new implmentation of the mEPN-3D notation
Miru (formerly known as BioLayout Express3D)
Cells and Organisms, Genome, Pathway
Genome Browser
UCSC Genome Browser
Genome
Semi-automatic Placement of 1O5W into a heterogeneous lipid bilayer
MembraneEditor
Cells and Organisms, Molecular
was used in Chimera to annotate the barrel structure of green fluorescent protein with its centroid, major axis (red arrow), and an enclosing cylinder (shown with green hoops). The BILD file green.bild was generated with the python program green.py using the coordinates in green.pdb. Gallery entry courtesy of Mike Ess, Yeast Resource Center, University of Washington.
UCSF Chimera
Molecular
Example MIM drawn with MIMTool
MIMTool
Molecular
A generic sunburst diagram: each block represents a node within a tree. The order and position of the blocks recreates the structure of the tree.
Sunburst view of in situ gene-expression data from EMAGE
Anatomy Physiology and Atlases, Genome
The inPHAP graphical user interface. It consists of six components which are highlighted with boxes of different color. Blue (1): The haplotype visualization panel providing color-encoded base information for phased haplotype or unphased genotype data, green (2): the subject meta-information panel next to the haplotype visualization panel, red (3): the SNV meta-information panel below the haplotype visualization panel, purple (4): the overview panel, displaying the viewers current focus in the haplotype vis
inPHAP
Genome
A view of LayerCake, showing 24 sequences, with each block of the color field aggregating 50 individual base pairs. Here the user has zoomed in on one such block, showing all reads for 50 base pairs simultaneously in a zoomed in area. The reference genome is repeated between each row for context. The user can further mouse over a particular column to see the identity of variants (in terms of base pairs) in each sequence in the histogram on the far right. Rows not within the zoom window are slightly “fogged”
LayerCake
Genome, Populations
TIALA's graphical user interface. View elements can be hidden or detached from their common context and all plots are connected to each other, such that a selection of genes in one plot automatically results in a selection in the other plots. A, The subset of chosen genes is visualized in a profile plot for each time series. The profile plots show the profiles of all available time points in the corresponding data set allowing users to simultaneously inspect the unaligned profiles and the aligned data in se
TIALA
Genome
Implicit clipping plane. a) The implicit function evaluates the molecular surface (green). It takes into account only atoms that intersect the plane or lie in the half-space defined by the plane (arrows). b) Protein Pr3 is colored according to the distance to the plane, where within range Formula the final color is interpolated as it is sketched by the blue rectangles in (a).
Physioillustration: Interactive molecular illustration
Anatomy Physiology and Atlases, Molecular
Comparison of culling efficacy between a skeleton octree with maximum depth 6 and the GPU based algorithm at 3 different distances. The scene consist of 100 neurons arranged in a vertical structure known as minicolumn. In every screenshot, the white inner square is the actual viewport; anything draw on the gray background is out of the view frustum.
Real-time Neuron Viz
Anatomy Physiology and Atlases
Table-based visualization of the MSA from the Abp2 family (PF09441) using the Clustal color-coding scheme. While the visualization of the first 10 sequences limited to the first 117 columns in the MSA provides both, focus and context (a), the visualization of the whole MSA makes the identification of features difficult Formula$(b)$
GVF Alignment Viz
Genome, Molecular