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Updated: May 28, 2026

A Graphical User Interface for Software-assisted Tracking of Protein Concentration in Dynamic Cellular Protrusions
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A Step-by-Step GUI-Based Protocol for Molecular Dating Analysis Using PhyloSuite v2.

Dong Zhao1,2, Ivan Jakovlić2, Xiantong Liu2

  • 1Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Xizang University, Lhasa, China.

Bio-Protocol
|May 27, 2026
PubMed
Summary
This summary is machine-generated.

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This study introduces PhyloSuite v2, a graphical user interface (GUI) workflow that simplifies molecular dating in genomics. It enhances analysis efficiency and accuracy for divergence-time estimation, making complex genomic research more accessible.

Area of Science:

  • Genomics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Genomic research faces challenges in molecular dating due to imperfect substitution models and rate heterogeneity.
  • Current molecular dating workflows are operationally demanding, requiring multiple tools and manual steps, leading to errors and high hands-on time.

Purpose of the Study:

  • To present a GUI-based workflow in PhyloSuite v2 to simplify molecular dating analysis.
  • To lower the operational barrier for users conducting molecular dating on genome-scale datasets.

Main Methods:

  • Utilized a fish nuclear genome dataset for demonstration.
  • Implemented a GUI workflow covering data import, fossil calibration configuration, automatic substitution model selection, and MCMC convergence assessment.
Keywords:
MCMCtreeMolecular datingPhyloSuite v2r8stimetree

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  • Automated complex analytical procedures and data visualization.

    • Main Results:

    • PhyloSuite v2 streamlines the entire molecular dating process, from input preparation to timetree visualization.
    • The workflow enhances efficiency and accuracy in divergence-time estimation and result verification.
    • Users can quickly master the protocol, improving reproducibility and diagnostic assessment.

    Conclusions:

    • PhyloSuite v2 significantly improves the efficiency and accessibility of molecular dating in genomic research.
    • The GUI-based approach reduces operational demands and potential errors in divergence-time estimation.
    • This protocol facilitates robust analysis and verification of molecular dating results.