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Related Experiment Video

Updated: Jun 15, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Jane: a new tool for the cophylogeny reconstruction problem.

Chris Conow¹, Daniel Fielder, Yaniv Ovadia

¹Department of Computer Science, California State Polytechnic University, Pomona, CA, USA.

Algorithms for Molecular Biology : AMB

|February 26, 2010

Summary

Jane is a new software tool that reconciles pairs of trees to study historical associations in fields like parasitology. It uses dynamic programming and genetic algorithms to find optimal solutions for complex cophylogenetic reconstruction problems.

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Last Updated: Jun 15, 2026

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Area of Science:

Evolutionary biology
Bioinformatics
Computational biology

Background:

The study of historical associations is crucial in fields like parasitology, molecular systematics, and biogeography.
Reconciling pairs of trees, considering biologically plausible events and costs, is a fundamental challenge.
Existing software tools have limitations, necessitating new approaches for cophylogenetic analysis.

Purpose of the Study:

To introduce Jane, a novel software tool designed for the analysis of historical associations by reconciling phylogenetic trees.
To provide a user-friendly interface for researchers to explore and modify solutions for cophylogenetic reconstruction.

Main Methods:

Jane employs a combination of polynomial time dynamic programming and a genetic algorithm.
The software allows for the incorporation of detailed timing information for host and parasite trees.
Users can define constraints such as host switch distance and region-specific host switch costs.

Main Results:

Jane efficiently finds highly accurate, often optimal, solutions for large tree pairs.
The tool facilitates interactive exploration and modification of cophylogenetic reconstructions through its graphical user interface.
Rich timing and cost information can be integrated into the analysis.

Conclusions:

Jane is a valuable tool for cophylogenetic reconstruction, complementing existing software.
Its advanced functionalities are expected to benefit researchers in parasitology, molecular systematics, and biogeography.
The software enhances the study of evolutionary relationships and historical associations between biological entities.