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Updated: May 1, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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Feature Frequency Profile (FFP) Method: A Language Model for Whole-Genome ("Organism") Phylogeny.

JaeJin Choi1, Byung-Ju Kim1,2, Sung-Hou Kim3

  • 1Department of Chemistry and Center for Computational Biology, University of California, Berkeley, CA, USA.

Methods in Molecular Biology (Clifton, N.J.)
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Summary
This summary is machine-generated.

Molecular phylogenetic methods have limitations in depicting organismal evolution. Whole-genome sequencing and analysis now enable more accurate evolutionary trees for life.

Keywords:
Feature frequency profile (FFP)Jensen–Shannon divergenceMolecular treeOrganism treePan-genomic Tree-of-Life (ToL)Rooting of ToLWhole-genome tree

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Area of Science:

  • Evolutionary Biology
  • Genomics
  • Bioinformatics

Background:

  • Molecular phylogenetic methods, relying on limited gene sequences, have dominated evolutionary studies for decades.
  • These methods have intrinsic limitations, as they infer molecule evolution, not organism or whole-genome evolution.
  • Technological and computational advancements were necessary for whole-genome-based phylogenetics.

Purpose of the Study:

  • To highlight the limitations of traditional molecular phylogenetic methods.
  • To introduce the potential of whole-genome-based phylogenetic analysis.
  • To present an example of a whole-genome Tree of Life.

Main Methods:

  • Review of limitations in traditional molecular phylogenetic approaches.
  • Discussion of technological advancements in whole-genome sequencing.
  • Explanation of computational developments for whole-genome sequence comparison.
  • Presentation of a whole-genome Tree of Life example.

Main Results:

  • Molecular phylogenetics primarily reflects the evolution of selected molecules, not whole organisms or genomes.
  • The recent emergence of economic whole-genome sequencing technologies, especially for eukaryotes, is a key development.
  • Advances in computational methods for efficient whole-genome sequence comparison are now available.
  • A whole-genome Tree of Life has been constructed as an example.

Conclusions:

  • Whole-genome phylogenetic analysis offers a more comprehensive approach to inferring organismal evolution.
  • The limitations of traditional molecular methods necessitate a shift towards genome-scale phylogenetics.
  • The presented whole-genome Tree of Life exemplifies the future direction of evolutionary studies.