> For the complete documentation index, see [llms.txt](https://cgps.gitbook.io/pathogenwatch/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cgps.gitbook.io/pathogenwatch/technical-descriptions-of-analysis-tools/lineage-and-genotyping/pangolin.md).

# Pangolin

## About

[Pangolin (**P**hylogenetic **A**ssignment of **N**amed **G**lobal **O**utbreak **LIN**eages)](https://github.com/cov-lineages/pangolin) is a tool provided by the Rambaut group as part of the COG-UK consortium for the assignment of lineage names to SARS-CoV-2 genomes.

## Method

Pangolin uses an internal machine learning-based method called Pangolearn to assign a lineage to query genomes. For a full description of how lineages are assigned see the description of Pangolearn: <https://github.com/cov-lineages/pangolin#pangolearn-description>.

## Viewing the output in Pathogenwatch

### Downloads, genome reports, and collections

The [complete output](https://github.com/cov-lineages/pangolin#output) is provided by the CSV download menu in the [Genome Browser](/pathogenwatch/how-to-use-pathogenwatch/browsing-and-viewing-genomes/browsing-searching-genomes.md) and the [Collection View](/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv.md). It is also shown in the Genome Reports for SARS-CoV-2 genomes (below) along with links to external descriptions of the lineages.

![Header and Typing section of a SARS-CoV-2 genome report.](/files/-MVaEK_heEQhe128T4jA)

### Browsing lineages

Pangolin lineages are displayed next to SARS-CoV-2 genomes in the Genome Browser and in the Typing table of collections. It's also possible to find genomes with a particular lineage in the Genome Browser by selecting "*Betacoronavirus*" in the "Genus" filter, "*Severe acute respiratory virus*" in the "Species" filter, and then "*subsp. SARS-CoV-2*". This enables the "Lineage" filter, allowing genomes from particular lineages to be selected.

![Selecting the B.1.177 lineage.](/files/-MVaH7qJiV3XAfw4pzTN)

## How to cite

O'Toole Á, Scher E, Underwood A, et al. Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool. *Virus Evol*. 2021;7(2):veab064. Published 2021 Jul 30. doi:10.1093/ve/veab064