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
SATORI's interface
SATORI
Genome
HiPiler's interface
HiPiler
Genome
MLCut
MLCut
Genome
Multi-view accessible with Listeriomics: Genomics, Transcriptomics, Proteomics, Genome Viewer, Co-expression Networks, Phylogeny, Small RNAs
Listeriomics
Cells and Organisms, Genome
SeqMonk
Genome
Supramap
Supramap
Genome
Epiviz
Epiviz
Genome
VisRseq
Genome
expVIP
expVIP
Genome
panX
Genome
gene.iobio.io
iobio
Genome
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
GenomeCRISPR concept
GenomeCRISPR
Genome
Hi-C Explorer
Genome
Mango interface
Mango
Genome
SynTView
Genome
PlantGenIE
Genome
CooccurViewer
Cells and Organisms, Genome
XCluSim
Genome
Pan-Tetris
Genome
Integrated Genome Browser
Integrated Genome Browser
Genome
Sequence Bundles web tool - screen capture
Sequence Bundles
Genome
Comparison of 29 bacterial genomes, colouring CDS by sequence identity to a reference genome.
GenomeDiagram
Genome
MI MatrixExplorer GUI
MI-MatrixExplorer
Genome, Phylogenetics
GeneProf
Genome, Molecular
Orchestral
Genome
Sequence logo viewer
Genome
Aequatus
Genome
TGAC Browser
Genome
Ensembl Genome Browser
Genome
SequenceJuxtaposer
SequenceJuxtaposer
Genome
Pipit
Pipit
Genome
Zomit
Zomit
Genome
ArkMAP
ArkMAP
Genome
GenotypeChecker
GenotypeChecker
Genome, Populations
Gremlin
Gremlin
Genome
Flapjack
Flapjack
Genome
a multiscale synteny browser for comparative genomics data
MizBee
Genome
Variant View
Variant View
Genome
Strudel
Strudel
Genome
Circos - Conservation
Circos
Genome
Pseudoviewer
Pseudoviewer 3
Genome, Molecular
Stratome X
StratomeX
Genome
Tableau
Tableau
Genome
IGV
IGV
Genome
molecular Screenshot with Autodesk Maya
Autodesk Maya
Cells and Organisms, 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
Paver example
Paver
Genome, Pathway
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
GenAMap is a visual analytics system for structured association mapping. It incorporates several different visualizations in a novel way to lead biologists to relevant SNPs and their associated traits. GenAMap enables biologists to explore the structure of the genome and trait data while exploring association strengths
GenAMap
Genome, Populations
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
A screenshot showing the iHat interface
iHAT
Genome
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
A screenshot of the NGS Overlap Searcher tool.
NGS Overlap Searcher
Genome
GTB dynamic filters applied to a feature/annotation track: (1) filtered for higher scoring features and (2) filtered for featues with higher FPKM (an abundance measure).
Galaxy Track Browser
Genome
A conserved operon examined using Gene-RiViT. Left(a): The RiViT view provides local context information about gene neighborhoods. Homologous genes are aligned in green. Genes shown in grey show that no homologs were found for an organism. Right(b): A zoomed view of the dot plot view shows a conserved operon for two query species. Five homologous genes are highlighted around a central selected gene. All other points are shaded grey to reduce visibility.
Gene-RiViT
Genome, Populations
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
COMBat applied to a dataset with 268 genes-annotated with in total 634 gene ontology (GO) identifiers [1]-on both the rows and the columns. Three property matrices are shown, in which each cell contains the set of GO identifiers that the corresponding genes have in common. Each cell is colored by the number of elements in the set as given by the colormap (see legend in the lower-left corner). The cell is gray if no data is associated with it. In the top-left corner, the initial, un-sorted property matrix is
COMBat
Genome
Construction of a Level 1 MoClo Module
MoClo Planner
Genome, Molecular
 Screenshot of our software after few analysis steps. Panel (A) contains the visualization widget and interaction tools, here four subnetworks are represented and our dedicated Bring & Go is used on an element. The neighborhood of that element is highlighted in all views. Panel (B) contains the exploration tree view. In that tree, the root node corresponds to the original data and each time an algorithm is applied on a node (i.e. a-sub-network), we create a son in the tree corresponding to the output of the
rNAV
Genome, Pathway
Matse
Genome, Pathway