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: cospeciation, duplication, duplication with host switch, loss, 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. Note that while this documentation refers to the trees as "host" and "parasite," Jane is also used to reconcile other pairs of trees such as species trees and gene trees.

New! eMPRess

The eMPRess tool (released in Fall 2020) has many powerful features and fast algorithms and is intended to replace Jane.

Jane 4

Jane 4 supports the following features and capabilities. For more information on how to use Jane, view the tutorial.

• Functionality:
  • Has a graphical tree builder for constructing host/parasite trees, their tip associations, and other annotations. (New to Jane 4)
  • Supports automatic resolution of polytomies. (New to Jane 4)
  • Provides support values on events. (New to Jane 4)
  • Allows the user to explore the impact of ranging the event costs. (New to Jane 4)
  • Supports multi-host parasites and multi-parasite hosts.
  • Reads both .tree and .nex file formats.
  • Allows five different event types including failure to diverge.
  • Supports preferential host switching through limited host switch distance and/or variable switching costs.
  • Uses time zone information to order events.
  • 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 many parameters of the genetic algorithm.
  • Is multi-threaded and can thus exploit multi-core architectures.
  • Has been successfully used to analyze pairs of trees with over 200 tips per tree.

To cite Jane, or For more information on the underlying algorithms used in Jane, please refer to the paper Jane: A New Tool for the Cophylogeny Reconstruction Problem, Algorithms for Molecular Biology 2010, 5:16.

Get Jane 4!

Jane 4 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 4 (Version 4.01, updated January 30, 2019)

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

Versions 4, 3, and 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.

Many research students have contributed to the design and implementation of Jane. The Jane 1 team was Chris Conow, Daniel Fielder, and Yaniv Ovadia. The Jane 2 team was Benjamin Cousins, John Peebles, Tselil Schramm, and Anak Yodpinyanee. Jane 3 is due to Kevin Black. Ben Fish also made theoretical conributions. The Jane 4 team was Jordan Ezzell, David Lingenbrink, Andrew Michaud, Ki Wan Gkoo, Rebecca Thomas, and Nicole Wein. Bea Metitiri, Lisa Gai, and Jason Yu also contributed to the project. Lilly Liu and Nisha Bhatia have worked on new features. Finally, Tim Buchheim has contributed to keeping Jane running on newer versions of Mac OS.

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.