New Tool SPRTA Revolutionizes Phylogenetic Analysis for Pandemics

Researchers at the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) and the Australian National University have developed a groundbreaking tool called SPRTA (SPR-based Tree Assessment). This innovative system offers a faster and more efficient way to evaluate the reliability of phylogenetic trees, which are essential for understanding the evolution and relationships of viral strains, particularly during pandemics.

The emergence of COVID-19 highlighted the challenges in constructing evolutionary family trees, known as phylogenetic trees, for the virus. With millions of genomes to analyze, traditional methods fell short in assessing the reliability of these trees. SPRTA addresses this critical gap, providing a scalable solution that can manage the vast datasets generated in times of widespread outbreaks.

Transforming Phylogenetic Assessment

Since 1985, scientists have heavily relied on Felsenstein’s bootstrap method to measure confidence in phylogenetic trees. This process requires repeated analyses, often hundreds or thousands of times, making it impractical for the extensive genomic data encountered during a pandemic. The new paper, published in the journal Nature, introduces SPRTA as a modern alternative capable of efficiently managing the immense datasets characteristic of large-scale disease outbreaks.

Nick Goldman, Group Leader at EMBL-EBI, emphasized the significance of this advancement: “For nearly 40 years, scientists have relied on the same method to measure confidence in evolutionary trees, but when faced with the scale of data we saw during the COVID-19 pandemic, the old method simply couldn’t cope. SPRTA gives us a fast, reliable way to understand which parts of these massive trees we can trust and to find the most plausible alternatives in regions of low confidence.”

Enhancing Outbreak Analysis

Traditional phylogenetic assessment methods focus on whether groups of samples, or clades, are well-supported by the collected data. However, for effective outbreak analysis, this approach is often insufficient. SPRTA adopts a more nuanced methodology by evaluating the likelihood that a given virus strain derives from a specific ancestor while also exploring alternative evolutionary pathways.

By virtually rearranging branches of the phylogenetic tree, SPRTA tests numerous possible scenarios and compares the fit of each against the existing data. It ultimately assigns a probability score that reflects the confidence researchers can have in each connection. As Nicola De Maio, Senior Scientist at EMBL-EBI, noted, “With SPRTA, we’re not just making phylogenetic tree-building faster, we’re making it smarter. It helps researchers understand which relationships are solid and where they need to be cautious, even when working with millions of genomes.”

SPRTA has been tested using over two million SARS-CoV-2 genomes, demonstrating its ability to highlight reliable sections of phylogenetic trees, flag uncertain sample placements often caused by incomplete data, and reveal credible alternative origins for specific branches.

The integration of SPRTA into MAPLE, a tool designed at EMBL-EBI for efficiently constructing large phylogenetic trees, enhances its accessibility. Additionally, SPRTA is available within IQ-TREE, one of the leading phylogenetic software packages used globally. By embedding this tool in established platforms, researchers worldwide can readily apply it for outbreak tracking, genomic surveillance, and evolutionary studies.

As the world continues to grapple with the implications of pandemics, the development of SPRTA represents a significant advancement in the field of evolutionary biology, paving the way for more effective responses in future health crises. The research underscores the importance of adapting scientific methodologies to meet the challenges posed by emerging infectious diseases.

For further details, refer to the study by Nicola De Maio in Nature, published on November 5, 2025.