Kei Ono, lead developer from UCSD’s Cytoscape project, remarked that at a recent meeting on visualization, there were no projects with desktop applications.
BioJS – Built by the folks at EBI, BioJS provides a series of components for visualizing sequence and structure information. Here’s a video from last year’s GMOD meeting that describes the project.
Cytoscape.js – The Cytoscape.js framework provides a means for visualizing networked biological data in a browser. With the latest release of the Cytoscape Java application you can now export network data in JSON format, and visualize it in a web page using the Cytoscape.js library.
JBrowse – This library makes it easy to create your own genome browser.
jsMol – Is a transpiled version of jMol that allows users to view 3D molecular structures without having Java installed.
jsMolEdit – a library for editing and viewing 2D chemical structures. The library makes use of GWT.
jsPhylosvg – is a library for rendering phylogenetic trees.
OneZoom – another library for rendering phylogenetic trees.
SMS – The rather unfortunately named, Sequence Manipulation Suite, is a library for manipulating sequence data.