Who is Jane?

Jane is a software tool for the cophylogeny reconstruction problem. The input to Jane is a file containing a "host" tree, a "parasite" tree, and a mapping of the tips of the parasite tree to tips of the host tree. The user may specify the costs of each of five types of events: cospeciations, duplications, host switches, losses, and failure to diverge. Jane then endeavors to find least cost mappings of the parasite tree onto the host tree subject to the given tip mapping.

Jane 3

Jane 3 supports the following features and capabilities. For more information on how to use Jane, view the tutorial.

• Functionality:
  • Reads both .tree and .nex file formats.
  • Recognizes two different cost models: edge-based and node-based.
  • Allows five different event types including failure to diverge. Failure to diverge allows reconstructions in which a parasite appears on multiple host tips.
  • Supports preferential host switching through limited host switch distance and/or variable switching costs.
  • Permits "time zone" annotations to specify the relative order of events in the host and parasite trees if known.
  • Provides both a graphical user interface and a command line interface.
  • Has an interactive solution viewer that allows the user to modify solutions and see the impact on cost.
  • Can statistically analyze solutions by comparisons with random samples.
• Performance:
  • Uses a heuristic approach, running a genetic algorithm with an internal fitness function that is evaluated using a dynamic programming algorithm. Jane is able to provide solutions that are always correct and often optimal (though optimal solutions are not guaranteed and it is believed that optimal solutions cannot be found in polynomial time since the cophylogeny reconstruction problems is known to be NP-complete).
  • Permits adjusting parameters of the genetic algorithm to achieve the desired balance of run-time performance and quality of solutions.
  • Multi-threaded to exploit multi-core architectures.
  • Has been successfully used by researchers to analyze pairs of trees with over 200 tips per tree.

For more information on the underlying algorithms used in Jane, please refer to the following papers:

• Jane: A New Tool for the Cophylogeny Reconstruction Problem, Algorithms for Molecular Biology 2010, 5:16.
  
• HMC Technical Report CS-2011-1

For more information about other cophylogeny software packages, see the Software Comparison page.

Get Jane 3!

Jane 3 is the latest version of Jane and it is freely available for research and educational purposes. It is open-source and distributed under a combination of the FreeBSD and Apache Software Foundation 2.0 licenses. (Some components are under the former, and some are under the latter.)

Jane is implemented in Java and runs on all platforms supporting Java 1.5 or higher. Jane can be downloaded as a platform specific application or a platform independent "JAR."

DOWNLOAD Jane 3

Documentation

• Frequently Asked Questions
• Tutorial
• Information on file formats read by Jane
• Choosing parameter values for Jane
• Explanation of Jane's cost models and events

Example Trees

Several example trees from the literature are available for download here.

Older Versions

Both Jane 3 and Jane 2 are available at the download page. Jane 1 can be found at the Jane 1 website.

Contact

Please contact Dr. Ran "RON" Libeskind-Hadas (click here to show e-mail address) with questions or comments regarding Jane.

Credits and Acknowledgements

Jane was developed in the research group of Prof. Ran "RON" Libeskind-Hadas at Harvey Mudd College with support from the U.S. National Science Foundation under grant 0753306 and from the Howard Hughes Medical Institute under grant 52006301.

The original version of Jane was designed, developed, and implemented by Chris Conow, Daniel Fielder, and Yaniv Ovadia. Jane 2 and its new algorithms were designed, developed, and implemented by Benjamin Cousins, John Peebles, Tselil Schramm, and Anak Yodpinyanee. Jane 3 was designed, developed, and implemented by Kevin Black.

Ran Libeskind-Hadas gratefully acknowledges the ongoing valuable research collaboration with Dr. Michael Charleston at the School of Information Technologies at the University of Sydney, Australia.