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Related Experiment Video

Updated: May 7, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Analyzing and synthesizing phylogenies using tree alignment graphs.

Stephen A Smith1, Joseph W Brown, Cody E Hinchliff

  • 1Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America.

Plos Computational Biology
|October 3, 2013
PubMed
Summary
This summary is machine-generated.

We introduce tree alignment graphs (TAGs) to analyze and synthesize multiple, conflicting phylogenetic trees. TAGs offer a novel way to explore evolutionary uncertainty and conflict, providing an alternative to traditional tree analysis methods.

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Last Updated: May 7, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

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12:00

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07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Area of Science:

  • Evolutionary biology
  • Phylogenetics
  • Bioinformatics

Background:

  • Phylogenetic trees are crucial for visualizing evolution but struggle with summarizing multiple trees, especially with conflicting data or phenomena like horizontal gene transfer.
  • Existing methods face challenges when dealing with datasets that have partially overlapping taxon sets or topological conflicts.

Purpose of the Study:

  • To develop a novel graph-based method for aligning, synthesizing, and analyzing sets of rooted phylogenetic trees.
  • To provide an alternative to consensus tree and supertree methods for handling complex phylogenetic datasets.

Main Methods:

  • Introduction of the tree alignment graph (TAG) framework for representing and analyzing sets of phylogenetic trees.
  • Demonstration of TAGs using bootstrap trees from the Angiosperm Tree of Life project to explore uncertainty.
  • Application of TAG synthesis for constructing a repeatable phylogenetic tree from bird study data.

Main Results:

  • TAGs effectively visualize and analyze uncertainty and conflict in phylogenetic datasets, revealing details missed by consensus trees.
  • Analysis of bootstrap trees showed that graph structures offer deeper insights into unresolved areas.
  • Synthesized TAGs provide a repeatable method for tree construction with updatable source information.

Conclusions:

  • Tree alignment graphs offer a tractable and powerful alternative to traditional phylogenetic tree analysis methods.
  • TAGs facilitate the exploration of complex evolutionary relationships and dataset structures.
  • This graph-based approach enhances the analysis of large-scale phylogenetic data and evolutionary patterns.