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.