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A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
35.2K
Pareto-optimal phylogenetic tree reconciliation.
Ran Libeskind-Hadas1, Yi-Chieh Wu1, Mukul S Bansal1
1Department of Computer Science, Harvey Mudd College, Claremont, CA 91711, Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269 and Broad Institute, Cambridge, MA 02142, USA.
Bioinformatics (Oxford, England)
|June 17, 2014
Summary
This study introduces an efficient algorithm and software for phylogenetic tree reconciliation, offering a systematic way to understand event costs and solutions. This improves evolutionary analyses and statistical testing in genomics and cophylogenetics.
Area of Science:
- Computational Biology
- Evolutionary Biology
- Bioinformatics
Background:
- Phylogenetic tree reconciliation reconstructs evolutionary histories using maximum parsimony and event costs.
- The relationship between event costs and reconciliation solutions is poorly understood.
- Selecting appropriate event costs for phylogenetic reconciliation is challenging.
Purpose of the Study:
- To develop a systematic method for understanding the relationship between event costs and phylogenetic reconciliations.
- To provide efficient algorithms for computing Pareto-optimal sets of reconciliations.
- To introduce new techniques for computing event support values and performing statistical tests in cophylogenetic analyses.
Main Methods:
- Developed an efficient algorithm for computing Pareto-optimal sets of reconciliations.
- Created new software tools implemented in Python.
- Demonstrated tool usage on evolutionary genomic and cophylogenetic datasets.
Main Results:
- The first systematic method for analyzing the impact of event costs on phylogenetic reconciliations.
- New techniques for calculating event support values.
- Enabled robust statistical tests for cophylogenetic analyses.
Conclusions:
- The developed algorithm and tools provide a novel approach to phylogenetic reconciliation.
- Facilitates a deeper understanding of evolutionary event costs.
- Enhances the accuracy and robustness of evolutionary and cophylogenetic studies.
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