Jane: A new tool for the cophylogeny reconstruction problem

This paper describes the theory and implementation of a new software tool for the study ofhistorical associations. This problem arises in parasitology (associations of hosts and parasites), molecularsystematics (associations of organisms and genes), and biogeography (associations of regions and organisms).The underlying problem is that of reconciling pairs of trees subject to biologically plausible events and costsassociated with these events.

Existing software tools for this problem have strengths and limitations, and theJane new tool described here provides functionality that complements existing tools.

Results: The Jane software tool uses a polynomial time dynamic programming algorithm in conjunction with agenetic algorithm to find very good, and often optimal, solutions even for relatively large pairs of trees. The toolallows the user to provide rich timing information on both the host and parasite trees.

In addition the user canlimit host switch distance and specify multiple host switch costs by specifying regions in the host tree and costsfor host switches between pairs of regions. Jane also provides a graphical user interface that allows the user tointeractively experiment with modifications to the solutions found by the program.

Conclusions: The Jane tool is shown to be a useful tool for cophylogenetic reconstruction.

Its functionalitycomplements existing tools and it is therefore likely to be of use to researchers in the areas of parasitology,molecular systematics, and biogeography.

Author: Chris ConowDaniel FielderYaniv OvadiaRan Libeskind-Hadas
Credits/Source: Algorithms for Molecular Biology 2010, 5:16

Published on: 2010-02-03

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