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A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
TOPD/FMTS: a new software to compare phylogenetic trees.
Pere Puigbò1, Santiago Garcia-Vallvé, James O McInerney
1Evolutionary Genomics Group, Biochemistry and Biotechnology Department, Rovira i Virgili University, Tarragona, Spain. ppuigbo@urv.cat
Bioinformatics (Oxford, England)
|April 27, 2007
Summary
This study introduces TOPD/FMTS software for comparing phylogenetic trees, offering new methods for evaluating evolutionary relationships. It uniquely handles trees with both orthologs and paralogs, enhancing evolutionary analysis.
Area of Science:
- Bioinformatics
- Computational Biology
- Evolutionary Biology
Background:
- Phylogenetic tree comparison is crucial for understanding evolutionary relationships.
- Existing software may have limitations in handling complex datasets, such as those with orthologs and paralogs.
Purpose of the Study:
- To introduce TOPD/FMTS, a novel software package for evaluating similarities and differences between phylogenetic trees.
- To provide a versatile tool that accommodates various comparison methods and handles complex evolutionary scenarios.
Main Methods:
- Implementation of new algorithms: Disagree method for identifying differing taxa and Nodal method for nodal information comparison.
- Inclusion of established methods: Partition, Triplets, and Quartets for tree comparison.
- Development of the From Multiple to Single (FMTS) program to compare trees with both orthologs and paralogs.
- Integration of randomization analysis to assess statistical significance against chance expectations.
Main Results:
- TOPD/FMTS offers a comprehensive suite of methods for phylogenetic tree comparison.
- The software successfully enables the comparison of trees containing both orthologs and paralogs, a significant advancement.
- Novel algorithms like Disagree and Nodal provide new ways to dissect tree discrepancies and similarities.
Conclusions:
- TOPD/FMTS is a valuable new software tool for phylogenetic tree analysis.
- Its ability to handle orthologs and paralogs broadens its applicability in evolutionary studies.
- The integrated randomization tests add robustness to the comparison results.
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