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Microbial Phylogeny01:28

Microbial Phylogeny

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...
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Related Experiment Video

Updated: May 16, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Stability analysis of phylogenetic trees.

Saad I Sheikh1, Tamer Kahveci, Sanjay Ranka

  • 1Department of Computer and Information Science and Engineering, University of Florida, FL 32611, USA. sheikh@cise.ufl.edu

Bioinformatics (Oxford, England)
|November 20, 2012
PubMed
Summary
This summary is machine-generated.

Phylogenetic tree estimates can be unstable. New measures assess tree stability by analyzing changes in sequence data, ensuring reliability even for large datasets with thousands of taxa.

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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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Area of Science:

  • Evolutionary biology
  • Computational biology

Background:

  • Phylogenetics is crucial for understanding organismal evolution.
  • Heuristic algorithms can estimate large phylogenetic trees but may lack robustness.
  • Assessing the stability and reliability of phylogenetic tree estimates is essential.

Purpose of the Study:

  • To develop and evaluate novel measures for assessing phylogenetic tree stability.
  • To identify reliable components within large phylogenetic trees.

Main Methods:

  • Defined measures to quantify tree, subtree, and taxon stability against input sequence variations.
  • Incorporated analysis at the nucleotide level for fine-grained assessment.
  • Validated measures on extensive published phylogenetic datasets.

Main Results:

  • Developed computationally feasible measures for assessing phylogenetic tree stability.
  • Demonstrated effectiveness on large-scale datasets with tens of thousands of taxa.
  • Measures can identify the most reliable parts of phylogenetic trees.

Conclusions:

  • The proposed measures provide a robust way to assess phylogenetic tree stability.
  • These tools are applicable to large datasets, enhancing confidence in evolutionary relationship reconstructions.