> 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/how-to-use-pathogenwatch.md).

# How to use Pathogenwatch

- [Using the documentation](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/using-the-documentation.md)
- [Uploads and Projects](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/uploads-and-folders.md)
- [Genome Uploads & Projects](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/uploads-and-folders/genome-uploads-folders.md): Description of the Upload page, file formats, and Projects page.
- [Projects](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/uploads-and-folders/folders.md): How to use the Pathogenwatch projects to manage your genomes
- [Browsing and Viewing Genomes](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/browsing-and-viewing-genomes.md)
- [Browsing & Searching Genomes](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/browsing-and-viewing-genomes/browsing-searching-genomes.md)
- [Viewing Genome Reports](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/browsing-and-viewing-genomes/genome-reports.md): Detailed reports on individual genomes.
- [Editing metadata](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/browsing-and-viewing-genomes/editing-metadata.md): How to edit the metadata of your genomes after upload
- [Collections](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections.md)
- [Using The Interactive Collection View](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv.md)
- [The Interactive Collection View](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/the-interactive-collection-view.md)
- [The Collection Header](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/the-collection-header.md): The header provides access to collection information, search and other utilities.
- [The Map Panel](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/map-panel.md)
- [The Tree Panel](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/tree-panel.md)
- [Tree Panel](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/tree-panel/tree-panel.md)
- [Generating a new tree](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/tree-panel/generating-a-new-tree.md)
- [Data Tables](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/data-tables.md)
- [The Timeline Panel](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/timeline.md)
- [Context search panel](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/context-search.md)
- [Legend, Labels, and Colours](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/legend-labels-and-colours.md)
- [Searching genomes in a collection](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/searching-genomes-in-a-collection.md)
- [Integrating private metadata](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/integrating-private-metadata.md): The collection viewer allows local-only analysis of confidential metadata
- [Creating sub-collections](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv/creating-sub-collections.md)
- [Creating & Sharing Collections](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/creating-sharing-collections.md)
- [Browsing Collections](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/collections/browsing-collections.md)
- [Genomic Neighbourhood Search](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/genomic-neighbourhood-search.md): The Pathogenwatch context search service
- [Context search overview](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/genomic-neighbourhood-search/context-search-overview.md): The basic of how the search tool works
- [Single genome seach](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/genomic-neighbourhood-search/single-genome-seach.md): How to generate a context for a single genome
- [Collection search](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/genomic-neighbourhood-search/collection-search.md): Exploring the genomic neighbourhood for a collection of genomes
- [The cluster viewer](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/genomic-neighbourhood-search/the-cluster-viewer.md): How to use the interactive cluster viewer
- [Downloading Data](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/downloading-data.md): How to download FASTAs, metadata and analysis results from Pathogenwatch
- [Deleting items](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/deleting-items.md)
- [Tips and Tricks](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/tips-and-tricks.md): Please contact us if you have Tips & Tricks to add to this page
- [The API](https://cgps.gitbook.io/pathogenwatch/how-to-use-pathogenwatch/the-api.md): Programmatic access to Pathogenwatch