We can’t really provide support for ITOL, since we don’t develop it, but, they have pretty nice docs that demonstrate how to prepare you annotation file.
Using the Moving Pictures dataset, I prepared a phylogenetic tree, with taxonomic annotations, for viewing in ITOL using the following procedure:
- Export QIIME 2 Artifacts
$ qiime tools export rooted-tree.qza --output-dir .
$ qiime tools export taxonomy.qza --output-dir .
rooted-tree.qza taxonomy.qza taxonomy.tsv tree.nwk
- Prepare annotation file (note, these commands use macOS
sed — if you are on a Linux machine you will need to adjust appropriately - you can also use MS Excel or LibreOffice to make this file)
$ echo $'LABELS\nSEPARATOR TAB\nDATA' > taxonomy.txt
$ sed "1d" taxonomy.tsv | cut -f1,2 >> taxonomy.txt
Here is what that file looks like after preparing it following the ITOL docs: taxonomy.txt (97.8 KB)
- Load the NWK file in ITOL, then add the annotation (
taxonomy.txt) by dragging-and-dropping onto the rendered tree graphic:
As I mentioned above, we can’t really provide support for ITOL, but hopefully this is enough to get you started!
taxa barplots visualization includes a drop-down that allows you to select a taxonomic level to view, here is the Moving Pictures tutorial at the genus level:
Please note that the “Taxonomic Level” dropdown is set to “Level 6”, which corresponds with the genus level in the Greengenes database.
If you haven’t had a chance to work through the Moving Pictures tutorial, I would highly recommend working through our Getting Started guide, which will get you geared up for QIIME 2!
Good luck and keep us posted!