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Updated: Jun 17, 2026
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Comparison of phylogenetic trees through alignment of embedded evolutionary distances
1Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. kbchoi@cs.unc.edu
BMC Bioinformatics
|December 17, 2009
Summary
A new method, xCEED, compares phylogenetic trees by aligning high-dimensional embeddings. This approach enhances the analysis of evolutionary relationships and biological processes, outperforming existing methods in predicting protein interactions.
Area of Science:
- Evolutionary biology
- Bioinformatics
- Computational biology
Background:
- Phylogenetic trees are crucial for understanding evolutionary relationships.
- Comparing phylogenetic trees to assess similarity and quantify biological processes is challenging.
Purpose of the Study:
- To introduce a novel method for comparing phylogenetic distance information.
- To provide a tool for measuring global similarity and incongruities between phylogenetic trees.
Main Methods:
- The xCEED (Comparison of Embedded Evolutionary Distances) methodology aligns representative high-dimensional embeddings.
- It employs multidimensional scaling and Procrustes-related superimposition techniques.
Main Results:
- xCEED measures global similarity and incongruities between phylogenetic trees.
- The method demonstrates improved performance in predicting coevolving protein interactions compared to existing approaches.
- It is applicable to detecting horizontal gene transfer and predicting interaction specificity in multigene families.
Conclusions:
- The developed approaches offer new tools for studying phylogenetic trees and evolutionary processes.
- Source code for xCEED is publicly available for further research and application.
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