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

MicrobeTrace is a free, secure, browser-based bioinformatics tool to integrate and visualize epidemiologic, laboratory, and molecular data for outbreak investigations, with over 14,000 users from 127 countries. Regular testing, user feedback, and comparison with other bioinformatics tools identified areas for improvement, prompting major architectural and functional upgrades. In MicrobeTrace 2.0, we refactored the codebase using Angular to improve scalability, performance, and usability. We also replaced the D3.js visualization engine with Cytoscape.js for faster, more efficient rendering of large networks. The update adds enhanced visualizations, new analytical tools, and expanded functionality within existing views. It also supports seamless integration with external phylogenetic platforms, such as Nextstrain and UShER (Ultrafast Sample Placement on Existing Trees), enabling users to import phylogenetic trees, visualize them as genetic networks, and securely enrich them with epidemiological and demographic metadata. These enhancements position MicrobeTrace as a next-generation, interoperable tool for genomic epidemiology and data-driven public health response.