It says’" Error: QIIME 2 plugin ‘phylogeny’ has no action ‘align-to-tree-mafft-fasttree’. I know align-to-tree-mafft-fasttree is a work-flow. I can I add this workflow?
Your virtualbox is new enough that you should be able to follow the install instructions for miniconda and then just edit your .bashrc file so that it doesn’t source the old one automatically. q2studio will remain out of date unless you get the new virtualbox image however.
Now, I have a tree name “rooted-tree.qza”. I’d like to know if I can view the tree in QIIME? For example, is it possible I convert this file to rooted-tree.qzv or convert to *.tre file and opened in other third-party software
We don’t have a good visualizer for trees at this time, but iTOL understands QIIME 2 artifacts.
You can also always export the data in any QIIME 2 artifact with qiime tools export. In this case you’ll get a newick file (aka .tre) from rooted-tree.qza.
Citing QIIME 2
If you use QIIME 2 in any published work, you should cite QIIME 2 and the plugins that you used. To display the citations for QIIME 2 and all installed plugins, run: