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Updated: Mar 27, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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Phyling: phylogenetic inference from annotated genomes.

Cheng-Hung Tsai1,2, Jason E Stajich1,3

  • 1Department of Microbiology & Plant Pathology, University of California-Riverside, Riverside, CA 92521, United States.

G3 (Bethesda, Md.)
|March 26, 2026
PubMed
Summary
This summary is machine-generated.

Phyling is a new tool for fast and scalable phylogenomic reconstruction using genomic data. It accurately infers species phylogenies, outperforming existing methods in speed and efficiency.

Keywords:
PEQG2026bacteriafungihidden Markov modelsorthologyphylogeneticsphylogenomicspythonsoftware

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Area of Science:

  • Genomics
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Phylogenomic reconstruction is crucial for understanding evolutionary relationships.
  • Existing methods can be computationally intensive and lack scalability for large datasets.

Purpose of the Study:

  • To develop a fast, scalable, and user-friendly tool for phylogenomic reconstruction.
  • To enable accurate species phylogeny inference directly from protein-encoded genomic data.

Main Methods:

  • Phyling identifies orthologous genes using Hidden Markov Models (HMM) profiles from the BUSCO database.
  • It incorporates a phylogenetic informativeness filter to optimize inference speed.
  • Automated species tree construction is supported via consensus or concatenation strategies.

Main Results:

  • Phyling demonstrates significantly faster performance compared to OrthoFinder.
  • It achieves equal or superior accuracy in phylogenetic reconstruction.
  • The tool optimizes memory usage and data processing for efficient handling of large phylogenies.

Conclusions:

  • Phyling offers an efficient and accurate solution for large-scale phylogenomic analyses.
  • Its user-friendly design and checkpoint system enhance usability and flexibility.
  • The tool supports both protein and nucleotide coding sequences for comprehensive phylogenetic signal capture.