Replicon discrimination
Systematic analysis across chromosomes, plasmids and viruses without collapsing biology into a single task.
ICTV-aligned taxonomy
Virus taxonomy inference aligned with the ICTV framework for interpretable, hierarchical organisation.
Functional modularity
Phage protein functional annotation, interpreted at modular and genome scales.
Why the mobile genetic element continuum matters
Mobile genetic elements (MGEs) — including chromosomes, plasmids and viruses — underpin microbial evolution, yet are typically analysed as discrete entities despite extensive genetic exchange and mosaic organisation. This fragmentation obscures transitional states, mixed replicons and biologically meaningful uncertainty.
A system, not a single task
PhageProfiler is an integrated framework that combines DNA- and protein-level analyses to study chromosomes, plasmids and viruses directly from genomic sequence data.
- Replicon discrimination across chromosomes, plasmids and viruses
- Virus taxonomy inference aligned with the ICTV framework
- Phage functional annotation at modular and genome scales
Task-aligned representations across biological levels
Different biological questions operate at different biological levels. PhageProfiler integrates task-specific DNA-level representations for replicon discrimination and viral taxonomy with protein-level representations for phage functional annotation, enabling coherent analysis across genome organisation, taxonomy and functional modularity while respecting their distinct analytical scopes.
Revealing lineage structure within the viral genomic landscape
Using persistent virulent phages as a system-level case study, PhageProfiler recovers structured, ICTV-aligned lineage organisation within the viral genomic landscape directly from sequence-derived representations, recapitulating known persistence-associated lineages while revealing additional persistence-compatible viral genera.
From genomes to global atlases
Applied to large-scale metagenomic data, PhageProfiler enables construction of a global virus–phage–plasmid atlas that delineates organisational structure, transitional zones and regions of potential novelty.
Together, these results illustrate how PhageProfiler functions not only as a set of analytical tools, but as an interconnected system for biological exploration.
Community & Contribution
PhageProfiler is fully open source under the MIT License.
Publications
Exploring the mobile genetic element continuum with PhageProfiler
Wang J., Ren J., et al. (2026). To be submitted.
title={Exploring the mobile genetic element continuum with PhageProfiler},
author={Wang, J., Ren, J., and et al.},
institution={University of Bath & EMBL-EBI},
year={2026}
}