Consider using tabs or accordions for all the different tree builder import options to reduce cognitive load.

Add a 'start new job' cta on the My Jobs page alongside the other buttons.

When generating a tree from an iNaturalist observation blast results, the query coverage, subject coverage, and identity sequence filters have the opposite sense from what I would expect given familiarity with blast metrics, i.e., 100 seems to be no filtering, 0 is strict filtering. Also, consider a conservative default on coverage to eliminate 5.8S-only matches.

Make a way to periodically refresh tree tip names so that they display the most up-to-date names

Add a button in tree viewer for a new tree

Add mycomap.org functionality since .com will be/is legacy content

Add some help to make it a little easier to use and make it so you can't compress all of the sequences together vertically

Make it easier to annotate trees in more ways.

Remove off-target sequences from trees by default when using mycomap source

The phylotree viewer shows some responsiveness issues during user interaction.Clicking on the black screen causes flickering effects.I suggest optimizing the UX for smoother user experience.

Make it easy to embed tree in iNaturalist observation

Implement adjusted identity from https//github.com/joshuaowalker/adjusted-identity

Import sequences from a list of Genbank accessions, for recreating trees from papers.

Have the option to add type sequences to the BLAST results / FASTA files that users upload.