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Updated: May 27, 2025

Author Spotlight: Advancements in X-ray CT Tool Chain for Tree Core Analysis
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Leveraging DAGs to improve context-sensitive and abundance-aware tree estimation.

Will Dumm1,2, Duncan Ralph1, William DeWitt3

  • 1Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA.

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
|February 20, 2025
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GCtree enhances phylogenetic inference by efficiently discovering diverse evolutionary trees using sequence abundance and novel objective functions. This improves accuracy for B-cell receptor data analysis.

Keywords:
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Area of Science:

  • Computational Biology
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Phylogenetic inference is crucial for understanding evolutionary relationships.
  • Existing methods like GCtree utilize sequence abundance for parsimony-based inference.
  • Previous studies demonstrated GCtree's competitive performance on B-cell receptor data.

Purpose of the Study:

  • To introduce recent enhancements to the GCtree phylogenetic inference package.
  • To improve the efficiency and accuracy of discovering diverse evolutionary trees.
  • To incorporate new objective functions for tree ranking and context-sensitive evolution modeling.

Main Methods:

  • Implemented an efficient tree storage data structure to discover additional parsimonious trees.
  • Developed a suite of new objective functions, including a Poisson context likelihood function.
  • Validated enhancements using simulated B-cell receptor data.
  • Benchmarked performance against other phylogenetic inference tools.

Main Results:

  • The new data structure discovers diverse parsimonious trees with minimal computational overhead.
  • The Poisson context likelihood function enables context-sensitive modeling of sequence evolution.
  • Enhanced GCtree shows competitive or improved performance on simulated B-cell receptor data.

Conclusions:

  • Recent enhancements significantly improve GCtree's capabilities for phylogenetic inference.
  • The updated GCtree offers a more powerful and efficient tool for analyzing sequence data, particularly for B-cell receptors.
  • These advancements contribute to the field of evolutionary modeling and phylogenetic analysis.