Wikiomics:Alignment visualization and plotting RNA structures

RNA Alignment visualization

 * 4SALE A tool for Synchronous RNA Sequence and Secondary Structure Alignment and Editing.
 * ConStruct Multipurpose tool for alignment editing, secondary structure prediction and visualizing RNA alignments (new version).
 * RALEE RNA ALignment Editor in Emacs.

Plotting RNA structures

 * loopDloop a tool for drawing RNA secondary structures in molecular biology.
 * jViz.Rna a Java application for visualizing and annotating RNA Secondary Structures
 * NAVIEW A group of programs and scripts that produce plots of RNA secondary structures. (Link Broken)
 * PseudoViewer Automatically visualizing RNA pseudoknot structures as planar graphs. Needs Windows .NET Framework for "in web" use, else exe is available.
 * RNAdraw an integrated program for RNA secondary structure calculation and analysis under 32-bit Microsoft Windows
 * RNAfamily A simple software tool that enables the display of all secondary structures for a family of RNA molecules. Uses a linear backbone representation.
 * RNAmovies a system for the visualization of RNA secondary structure spaces.
 * RNAplot Draw RNA Secondary Structures. Available formats are: PostScript (ps), Graph Meta Language (gml), Scalage Vector Graphics (svg), and XRNA save file (xrna).
 * RNAView/RnamlView generates 2-dimensional displays of RNA/DNA secondary structures with tertiary interactions.
 * RnaViz A user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules.
 * SStructView a Java applet for viewing RNA secondary structures and linking to multiple computational backends.
 * StructureLab An integrated graphical software tool for predicting, plotting and analyzing RNA secondary structures.
 * VARNA A Java lightweight Applet dedicated to drawing the secondary structure of RNA. It is also a Swing component that can be very easily included in an existing Java code working with RNA secondary structure to provide a fast and interactive visualization.
 * XRNA a Java based suite of tools for the creation, annotation and display of RNA secondary structure diagrams.