Visualizing phylogenetic trees

Hello forum.
There is currently no visualizer for trees, but you can export the RootedPhylogeny as a .nwk that can be opened in other programs. The problem is the tree is annotated with the feature IDs, when ideally it would have taxonomy. The tree is also rather big, so is there a way to filter out less abundant taxa from the tree?

Hi @MaxEdge,

Have you checked out the Empress plugin, yet? It's got all kinds of cool options for phylogenetic tree visualization and integrates directly with your qiime2 artifacts.

Can you rother programs not take a metadata file? Your taxonomy file should link to the tip IDs. The problems are that taxonomy is a many-to-one relationship, where multiple ASVs can have different taxonomic assignments. Also that morphology based taxonomy doesnt actually line up with phylogenetic history, and so you might discover not all the Firmicutes are in the same clade. (Although I think its is at least denoted in Greengenes2/GTDB, depending on your preferences). However, either way, you're not going to have unique names.

The phylogeny plugin is designed to interact with trees. The filter-tree method takes an input tree and a metadata file (including a filtered feature table) and will prune your tree so you only retain the tips of interest.



Hi, and thank you so much for the quick and detailed response!
I wasn't aware of the Empress plugin, and it pretty much does everything I want it to. The only real issue is it doesn't label nodes or the barplot, but rather gives a color legend.

When I said program, I was really more referring to online tools, such as NCBI tree viewer, ETE toolkit, IceTree, which take .nwk files, but none of them have an option for linking a taxonomy.tsv file. If you know of a better program for this, I'd be eager to hear about it.