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Related Experiment Video

Updated: Jan 7, 2026

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MicrobeTrace 2.0: the enhanced visualization multitool for molecular epidemiology and bioinformatics.

Anupama Shankar1, Evan Moscoso2, David Cowan1

  • 1Laboratory Branch, Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA.

Molecular Biology and Evolution
|January 1, 2026
PubMed
Summary
This summary is machine-generated.

MicrobeTrace 2.0 is an upgraded bioinformatics tool for outbreak investigations. It now offers enhanced visualizations and integrates with phylogenetic platforms for improved genomic epidemiology.

Keywords:
bioinformaticsdata analytics and visualizationmolecular epidemiologyoutbreak investigationsplatform interoperabilitysoftware

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Area of Science:

  • Bioinformatics
  • Genomic Epidemiology
  • Public Health

Background:

  • MicrobeTrace is a widely used, free, secure bioinformatics tool for integrating and visualizing outbreak investigation data.
  • Over 14,000 users across 127 countries rely on MicrobeTrace.
  • User feedback and testing identified needs for architectural and functional improvements.

Purpose of the Study:

  • To present the major upgrades in MicrobeTrace 2.0, focusing on architectural and functional enhancements.
  • To improve scalability, performance, and usability for outbreak investigations.
  • To enhance integration capabilities with external phylogenetic analysis tools.

Main Methods:

  • Refactored the codebase using Angular for improved performance and scalability.
  • Replaced the D3.js visualization engine with Cytoscape.js for efficient rendering of large networks.
  • Integrated support for external phylogenetic platforms like Nextstrain and UShER.

Main Results:

  • MicrobeTrace 2.0 features enhanced visualizations and new analytical tools.
  • The tool now supports seamless import and visualization of phylogenetic trees.
  • Users can enrich imported phylogenetic data with epidemiological and demographic metadata.

Conclusions:

  • MicrobeTrace 2.0 is a significantly improved, next-generation tool for genomic epidemiology.
  • The enhancements position MicrobeTrace as a key interoperable platform for data-driven public health response.
  • The tool facilitates a more comprehensive analysis of infectious disease outbreaks.