Pangolin
Phylogenetic Assignment of Named Global Outbreak Lineages
The primary software tool for assigning SARS-CoV-2 genome sequences to Pango lineages. Trusted by researchers and public health agencies worldwide for accurate, rapid lineage classification.
What is Pangolin?
Pangolin is an open-source software tool that assigns the most likely Pango lineage to SARS-CoV-2 query sequences. Using machine learning models and phylogenetic placement algorithms, it provides rapid, accurate lineage classification essential for genomic surveillance.
Fast Analysis
Process thousands of sequences quickly using optimized algorithms and models.
Accurate Results
High-accuracy lineage assignments validated against gold-standard designations.
Updated Daily
pangolin-data is updated regularly with new lineage definitions.
Open Source
Free to use under GPL-3.0 license. Contribute on GitHub.
Installation
Pangolin can be installed via Bioconda (recommended) or pip. It requires Python 3.8+ and works on Linux, macOS, and Windows (via WSL).
Install via Conda (Recommended)
The easiest method with all dependencies managed automatically.
Update pangolin-data
Keep your lineage definitions current with regular updates.
Run Analysis
Process your FASTA files with a single command.
seq1,JN.1.1,0.0,0.12,JN.1-like,...
seq2,BA.2.86,0.0,0.08,BA.2.86-like,...
How Pangolin Works
Pangolin uses a multi-step pipeline to assign lineages with high accuracy.
Input Processing
FASTA sequences are validated and aligned to the reference genome.
Scorpio Check
Sequences are scanned for constellation patterns to identify VOCs.
UShER Placement
Sequences are placed on a global phylogenetic tree using UShER.
Output Report
CSV report with lineage assignments, confidence scores, and QC metrics.
Output Format
Pangolin outputs a detailed CSV report with multiple fields for each sequence.
| Field | Description |
|---|---|
| taxon | Sequence name from the input FASTA file |
| lineage | Assigned Pango lineage (e.g., JN.1.1, BA.2.86) |
| conflict | Phylogenetic conflict score (lower is better) |
| ambiguity_score | Ambiguity in assignment (lower is better) |
| scorpio_call | Constellation-based variant call (e.g., Omicron-like) |
| scorpio_support | Support score for constellation match |
| scorpio_conflict | Conflict in constellation assignment |
| scorpio_notes | Additional notes on the assignment |
| version | Pangolin and data versions used |
| pangolin_version | Pangolin software version |
| scorpio_version | Scorpio version |
| constellation_version | Constellation definitions version |
| is_designated | Whether lineage is officially designated |
| qc_status | Quality control status (pass/fail) |
| qc_notes | Quality control notes |
| note | Additional processing notes |