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
HiPiler's interface
HiPiler
Genome
SeqMonk
Genome
HaptiMOL
HaptiMOL
Molecular
Reactome
Pathway
xiNET
xiNET
Molecular
OneZoom - mammals
OneZoom
Phylogenetics
FigTree
FigTree
Phylogenetics
VisRseq
Genome
panX
Genome
Annotools overview
Annotools
Genome
Hi-C Explorer
Genome
cellVIEW
Molecular
Mango interface
Mango
Genome
SynTView
Genome
Pan-Tetris
Genome
Molecular Maya molecular modeling simulation intuitive
Molecular Maya
Molecular
Integrated Genome Browser
Integrated Genome Browser
Genome
GraphiteLifeExplorer
GraphiteLifeExplorer
Molecular
OMERO
SequenceJuxtaposer
SequenceJuxtaposer
Genome
A tanglegram between a phylogeny of sections of Ficus (a) and that of their associated genera of pollinating wasps (b). Adapted from (Machado et al., 2005).
NN-tanglegram
Phylogenetics
ArkMAP
ArkMAP
Genome
GenotypeChecker
GenotypeChecker
Genome, Populations
BioFabric
BioFabric
Pathway
PhyloDet
PhyloDet
Phylogenetics
Dendroscope
Dendroscope
Phylogenetics
Variant View
Variant View
Genome
Strudel
Strudel
Genome
Pseudoviewer
Pseudoviewer 3
Genome, Molecular
Stratome X
StratomeX
Genome
Tableau
Tableau
Genome
IGV
IGV
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
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
A screenshot showing the iHat interface
iHAT
Genome
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
 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