Using the Taxonium desktop app#

Loading very large (>5M tips) trees in Taxonium works better in the desktop application. Whereas the Taxonium web app is limited when loading custom JSONL files by the browser’s memory limitations, the Taxonium desktop app runs a backend which can use much more memory to load larger trees and run more smoothly.



You can download the Taxonium desktop app for Windows, MacOS, or Linux from the releases page.


On MacOS you may need to “unquarantine” the app, because the code has not been signed. Please refer to the instructions on this page for how to do this.

Briefly, you can either navigate to the Applications folder and control-click on the Taxonium icon, then press Open, or you can use the Terminal:

sudo xattr -r -d "/Applications/"

(if Taxonium is stored at that location)

Using the app#

Once you have downloaded the app, point it to a Taxonium .jsonl or .jsonl.gz file and wait for the backend to load.

You can find a small example jsonl file here (right-click and save-as), or download the large Cov2Tree tree here (which is based on the UCSC public tree).


The Taxonium desktop app still requires an internet connection at present, which it uses to load the client.


On some systems, the app may prompt you to allow it to receive incoming connections. This is essential for functionality.

Creating JSONL files for the Taxonium desktop app#

The desktop app at present only supports Taxonium JSONL files. To create JSONL files you can use usher_to_taxonium or newick_to_taxonium.