Who is Jane?

Jane is a software tool for the cophylogeny reconstruction problem. It uses a novel approach coupling dynamic programming with a genetic algorithm.

Jane complements existing tools such as TreeMap (using the Jungles method) and Tarzan.

While TreeMap finds optimal solutions, its algorithm has exponential running time in the worst case. Therefore, TreeMap is primarily useful for relatively small trees. Tarzan uses a heuristic approach that is very fast and often finds excellent solutions, but can fail to find solutions when they exist and sometimes reports incorrect solutions (see Documentation of Timing Incompatibilities in Tarzan).

Jane's algorithm is slower than Tarzan's but fast enough to find solutions to relatively large problems in seconds to hours. Jane is multi-threaded and can exploit multi-core architectures. Moreover, Jane provides some functionality that is not found in other tools including the ability to:

• Set time zone ranges on both the host and parasite trees.
• Limit host switch distance.
• Define "regions" in the host tree and specify different host switch costs between each pair of regions.
• Browse and modify solutions interactively.

Get Jane

Jane is freely available for research and educational purposes. It is open-source and distributed under the FreeBSD software license.

Jane is implemented in Java and runs on all platforms supporting Java 1.5 or higher. Jane comes in a "jar" file and thus installing Jane is effortless.

Click here to register and download

Example Trees

Documentation

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