A comprehensive suite of open-source bioinformatics tools for SARS-CoV-2 genomic surveillance. From lineage assignment to outbreak investigation.
Phylogenetic Assignment of Named Global Outbreak Lineages
The primary software tool for assigning SARS-CoV-2 genome sequences to Pango lineages. Used worldwide for accurate, rapid lineage classification.
Serious Constellations Of Reoccurring Phylogenetically-Independent Origin
A tool for rapid classification of SARS-CoV-2 sequences using mutation constellations. Essential for detecting variants of concern (VOCs).
Cluster Investigation and Virus Epidemiology Tool
A powerful tool for rapid outbreak investigation. Generates comprehensive reports with phylogenetic trees, maps, timelines, and statistical summaries.
Phylogenetic Cluster Analysis Tool
A tool for identifying and flagging clusters in phylogenetic data. Designed for real-time genomics workflows with configurable statistical thresholds.
Our tools work together seamlessly for comprehensive genomic surveillance. Pangolin uses Scorpio for constellation detection, while Civet and Polecat provide complementary analysis capabilities.
Use our online analysis platform or download the tools for local use.
