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The unique PDN ecosystem connects a set of leading knowledgebases and tools that support the full lifecycle of pathogen data – from infrastructure to genomic analyses, evolution biology and surveillance and data discovery. It also supports their adoption through dedicated training.
Key figures
Patent mentions:
480
Cumulative; source: lens.org
Citations in peer-reviewed papers:
14 754
Cumulative citations of reference papers;
source: Web of Science
User countries:
180+
Source: Google Analytics
Which PDN resource should I use?
I want to…
Understand virus biology
Go to: ViralZone
Store or manage pathogen data
Go to: Loculus
Assign lineages or clades
Go to: Nextclade
Track pathogen evolution
Go to: Nextstrain / GenSpectrum
Perform advanced evolutionary analyses
Go to: BEAST2
Study deep viral evolution
Go to: FoldTree
Data & Knowledge Discovery
GenSpectrum
Unique value
Interactive exploration and analysis of pathogen sequences
Typical use cases
- Track variant frequencies across genomes
- Explore mutation co-occurrence patterns
- Analyze genomic signals in wastewater surveillance
PDN developments
- User-defined variant collections
- Improved user interface
- Interactive wastewater dashboards for SARS-CoV-2 and RSV
Links to other PDN resources
Loculus • Nextclade • Nextstrain • V-pipe
Evolution & Spread
FoldTree
Unique value
AI-driven analysis of viral evolution using predicted protein structures.
Typical use cases
- Compare viral proteins using structural features
- Identify structural core genes across viruses
- Reconstruct deep viral phylogenies
PDN developments
- Retraining protein language models with viral structure datasets
- Prediction of structural tokens from viral sequences
- Identification of structural core genes
Links to other PDN resources
ViralZone
Evolution & Spread
Nextstrain
Unique value
Real-time visualization and analysis of pathogen evolution using genomic data.
Typical use cases
- Visualize pathogen phylogenies
- Track pathogen spread and evolution
- Explore genomic diversity over time
PDN developments
- Methods to infer phylogenetic trees constrained by hierarchical nomenclature systems
- Improved scalability for large genomic datasets
Links to other PDN resources
BEAST2 • GenSpectrum • Nextclade • V-pipe
Evolution & Spread
BEAST2
Unique value
Statistical framework for evolutionary analysis of pathogen genomes.
Typical use cases
- Infer evolutionary relationships
- Model pathogen population dynamics
- Study bacterial evolution including horizontal gene transfer
PDN developments
- New phylogenetic network inference algorithms operators for recombining bacteria and viruses
- Simulation validation and proof-of-concept analyses
Links to other PDN resources
Loculus • Nextclade • Nextstrain • V-pipe
Training
Data & Knowledge Discovery
ViralZone
Unique value
Knowledgebase on virus biology and viral proteins.
Typical use cases
- Explore virus taxonomy and biology
- Study viral protein functions
- Compare viral proteins across virus families
PDN developments
- Pipeline to split viral polyproteins enabling structure-based analyses
- Pilot implementation for Flaviviridae
- Structure-based refinement of ViralZone taxonomy
Links to other PDN resources
FoldTree • V-pipe
Training
Fair Data Management
Loculus
Unique value
Scalable infrastructure for storing and managing pathogen genomic data.
Typical use cases
- Store and manage pathogen genomic sequences and metadata
- Enable programmatic access to and advanced searching of pathogen data
- Support genomic surveillance platforms (e.g. Pathoplexus)
PDN developments
- Support for multiple viruses sub-types within a single database
- Improved handling of segmented viruses
- Development of a more flexible API
Links to other PDN resources
GenSpectrum • Nextclade • Nextstrain
Genomic Analyses
V-pipe
Unique value
Pipeline for processing viral sequencing data and detecting genomic variation.
Typical use cases
- Analyze viral sequencing reads
- Detect mutations in viral populations
- Generate datasets for downstream analyses
Links to other PDN resources
GenSpectrum • Nextclade • Nextstrain • ViralZone
Training
Genomic Analyses
Nextclade
Unique value
Standardized clade assignment and quality control for viral genomes.
Typical use cases
- Assign viral genomes to clades
- Perform genome quality control
- Prepare data for phylogenetic analyses
PDN developments
- Updates to nomenclature and reference datasets for: SARS-CoV-2, Influenza, RSV, Mpox
Links to other PDN resources
BEAST2 • GenSpectrum • Nextstrain • V-pipe
Genomic Analyses
IMMense
Unique value
Genomic analysis workflows for fungal and bacterial pathogens, including antimicrobial resistance detection.
Typical use cases
- Analyze and quality control fungal / bacterial genome data
- Detect antimicrobial resistance mechanisms
- Process pathogen data from metagenomic samples
PDN developments
- Expansion to long-read sequencing data (incl. Candida species)
- Dedicated module for Mycobacterium tuberculosis
- Improved support for metagenomic inputs such as wastewater
- Dedicated fungal WGS pipeline
Links to other PDN resources
GenSpectrum • Nextstrain
Fair Data Management
Capacity Framework
Unique value
Structured framework to guide the implementation and assessment of FAIR pathogen data-sharing infrastructures and metadata standards.
Typical use cases
- Build pathogen data-sharing platforms
- Adopt metadata standards for genomic surveillance
- Align platforms with FAIR data practices
PDN developments
- Launch of the first version of the capacity framework
Links to other PDN resources
Loculus
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