Labeling phylogenies is critical for branch-level analyses such as RELAX and BUSTED. These instructions detail the most basic usage of the phylotree.js widget's branch labeling functionality.

1. Upload your phylogeny.
   • Click the Newick dropdown menu at the top left of the site and choose your newick-formatted phylogeny to upload. Once uploaded, the phylogeny will load in the widget for labeling and/or manipulation.
2. In the text box next to the Tag dropdown menu, create all of your labels before selecting/highlighting any branches.
   • By default, the first label will always be named Foreground. This can be renamed with Tag->Rename selection set as desired. Be sure to click Save when finished renaming!
   • To additional more labels, click Tag->New selection set. Each new selection set will be named, by default, new_selection_name. You can change this name now by directly typing the new name into the text field next to the Tag button. Again, click Save when finished renaming.

3. After all labels have been created, they will be visible in differently-colored text under the Tag dropdown menu. To select branches for a label, follow these steps:

   • Click the label of interest in the Tag dropdown menu. The name of your chosen label will now be shown in the text box to the right of Tag.
   • Highlight and select any branches for this label.
   • When finished, navigate back to Tag to select the next label of interest, and select branches accordingly. Proceed until all selections are complete.

4. Export your labeled phylogeny by clicking the Newick dropdown menu and then Export. A text box with your labeled newick tree will appear. Copy and paste this newick tree as needed.