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JSmol is the extension of the Java-based molecular visualization applet Jmol (jmol.sourceforge.net) as an HTML5 JavaScript-only web app. It can be used in conjunction with the Java applet to provide an alternative to Java when the platform does not support that (iPhone/iPad) or does not support applets (Android). Used in conjunction with the Jmol JavaScript Object (http://wiki.jmol.org/index.php/Jmol_Javascript_Object), JSmol seamlessly offers alternatives to Java on these non-Applet platforms.
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Wiggle is a client-side JavaScript program for aligning stereoscopic image sets and a Flash applet for viewing them. Authoring WiggleSets requires only a JavaScript browser, and a browser with Flash plugin (6+) is all that is needed to view the output.