Treenome Browser#

The Treenome Browser allows simultaneous exploration of a reference genome, phylogeny, and the genetic variation within a tree.

Getting Started#

Enabling the Treenome Browser#

Note

Currently, only jsonl trees that have been created with usher_to_taxonium using a protobuf and an associated Genbank file work with the Treenome Browser. E.g., usher_to_taxonium -i input.pb -o output.jsonl.gz --genbank gbfile.gb

If your supplied tree file is supported, enable Treenome Browser in the right-hand panel.

https://user-images.githubusercontent.com/6502785/182260804-29e238a0-fe18-4e07-8f45-0046ee47a4c3.png

Navigating the Treenome Browser#

To explore the tree, see the main Taxonium documentation

To explore the genome, click and drag (or scroll) left or right in the top (JBrowse) panel. Zoom into a region by entering coordinates or by dragging across a section of the genome. Hover over mutations to view details.

https://user-images.githubusercontent.com/6502785/182264410-eb760791-3d16-4162-bc94-1c83515a64fd.png

Amino acid mutations are enabled by default. You can also enable nucleotide mutations in the settings menu.

https://user-images.githubusercontent.com/6502785/182264641-d732e67d-cccd-4186-b40b-3a37a2cecffe.png

Loading annotations#

Load annotations by clicking the track selector button in the browser panel.

https://user-images.githubusercontent.com/6502785/182264983-c62d6f13-2323-46ba-872a-2db2ac864ca5.png

If you are viewing the public SARS-CoV-2 tree (cov2tree.org), annotation tracks are loaded automatically from the UCSC Genome Browser. Otherwise, annotations are currently limited to a reference sequence track.