Hope College Animations - http://www.cs.hope.edu/alganim/ Online animations of algorithms and data structures.
JFLAP, JAWAA, jeLLRap -- Visual and Interactive Tools - http://www.cs.duke.edu/~rodger/tools/tools.html Tools (Java programs) for visualizing and interacting with theoretical computer science concepts. JAWAA is a tool for creating algorithm animations on the web.
Opsis - http://opsis.sourceforge.net A Java applet designed to teach binary search tree algorithms. It is unique in the way it combines programming, proof, and animation to enhance the learning experience.
Backtracking - http://www.faust.fr.bw.schule.de/mhb/backtrack/backtren.htm A combinatorial puzzle is presented making visible the performance of a backtracking algorithm (requires JavaScript).
Sort Algorithms Visualizer - http://thomas.baudel.name/Visualisation/VisuTri/ Applet and web site for teaching sort algorithms. Includes animation of 11 algorithms and some in-depth studies.
LYDIAN - http://www.cs.chalmers.se/~lydian/ Simulation and visualization environment for distributed algorithms that provides students with an experimental environment to test and visualize the behaviour of distributed algorithms.
3 Sorts of Sort CAL Package - http://www.csis.ul.ie/modules/cs4111/3sorts/ Several sorting algorithms explained using a nice playing card based interface.
Leonardo - http://www.dis.uniroma1.it/~demetres/Leonardo/ An integrated C programming environment for reversible execution and logic-based software visualization developed at the University of Rome "La Sapienza".
Graph Animations with Combinatorica - http://www.cs.sunysb.edu/~skiena/combinatorica/animations/ Animations of several important graph-theoretic topics and algorithms.
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