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.
Researchers interested in cophylogenetic analysis, and tree reconciliation in particular, should also examine the Xscape suite of tools which complement Jane's functionality.
Jane 4 supports the following features and capabilities. For more information on how to use Jane, view the tutorial.
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.
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 May 30, 2013)
Several example trees from the literature are available for download here.
Please contact Dr. Ran "RON" Libeskind-Hadas (click here to show e-mail address) with questions or comments regarding Jane.
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.
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.