Phylogenetic table with lablels

[arsalane1978 (ekarsalan)]

Dear Qiime2 team / users,
Thank you for maintaining and updating the forum. I have a naive question as a new commercial to the field. Is there any way to visualize the fast tree rooted tree while labels are actual scientific taxonomic names rather than Qiime2 generated IDs?
Many thanks in advance

[jairideout (Jai Ram Rideout)]

Hi @arsalane1978! QIIME 2 doesn't currently support visualizing phylogenetic trees. You can export a Newick tree file from the .qza file and load the Newick file into a tree-viewing program of your choice (e.g. iTOL, FigTree, Archaeopteryx). You can also export the associated taxonomy annotations into a TSV file, which can be used to annotate tips in the tree.

Since we don't develop these external tree viewing programs, we can't provide official support for those tools here. However, these forum topics may be useful to get your tree and taxonomy files exported and loaded into iTOL:

Loading Greengenes tree in iTOL

Hi, Did anyone figure out the solution for this? Basically, 97_otus tree can be visualized in ITOL, but it seems the internal ids and annotation already in the tree are not being recognized by ITOL. Adding an external annotation file only shows Archaea, possibly due to limit on tips as someone mentioned above. Finally, how can we display bar charts for genus level using the greengenes trees? Thanks.

Tree visualization

Hi, I got the rooted.tree from qiime2, but it is a qza file. May I know how to change it into a qzv file, which can be visualized. OR change the qza file into a fasta file, which I can know the reads and draw a tree? Because all the qza file is not readable. Thanks so much.

Hope this helps!