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Jane: A New Tool For The Cophylogeny Reconstruction Problem, Chris Conow, Daniel Fielder '11, Yaniv J. Ovadia '10, Ran Libeskind-Hadas
Jane: A New Tool For The Cophylogeny Reconstruction Problem, Chris Conow, Daniel Fielder '11, Yaniv J. Ovadia '10, Ran Libeskind-Hadas
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Background
This paper describes the theory and implementation of a new software tool, called Jane, for the study of historical associations. This problem arises in parasitology (associations of hosts and parasites), molecular systematics (associations of orderings and genes), and biogeography (associations of regions and orderings). The underlying problem is that of reconciling pairs of trees subject to biologically plausible events and costs associated with these events. Existing software tools for this problem have strengths and limitations, and the new Jane tool described here provides functionality that complements existing tools.
Results
The Jane software tool uses a polynomial time dynamic …