> 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/using-the-documentation.md).

# Using the documentation

Pathogenwatch provides a range of different functions integrated with powerful interactive visualisation tools. Here we describe in detail each feature of the application and explain potential uses.

{% hint style="info" %}
**Navigating the documentation: Use the sidebar (left) to select different pages. Use the table of contents (right, shows when the page has headers) to jump to a specific section on the page.**
{% endhint %}

Visit the individual documentation pages for [Uploading ](/pathogenwatch/how-to-use-pathogenwatch/uploads-and-folders/genome-uploads-folders.md)data, Browsing [genomes ](/pathogenwatch/how-to-use-pathogenwatch/browsing-and-viewing-genomes/browsing-searching-genomes.md)& [Collections](/pathogenwatch/how-to-use-pathogenwatch/collections/browsing-collections.md), [creating collections](/pathogenwatch/how-to-use-pathogenwatch/collections/creating-sharing-collections.md) of your own, and understanding the [technical descriptions of the analysis tools](/pathogenwatch/technical-descriptions-of-analysis-tools.md) run within Pathogenwatch, as well as exploring collections visually with the [Interactive Collection View](/pathogenwatch/how-to-use-pathogenwatch/collections/using-the-icv.md).

For an overview of the application, visit the Brief Tour below: 

{% content-ref url="/pages/uLEU86HbwPRYykX5W0Ty" %}
[A Brief Tour of Pathogenwatch](/pathogenwatch/getting-started/a-brief-tour-of-pathogenwatch.md)
{% endcontent-ref %}

Otherwise, our FAQ (Frequently Asked Questions) may be useful.

{% content-ref url="/pages/MZ27LWy6Vs8L5e1qJnP5" %}
[FAQ](/pathogenwatch/faq.md)
{% endcontent-ref %}