merge rooted.qza trees

Hi Qiimers
Kindly assist in a command to merge rooted-tree.qza
merging with feature table commands for table.qza, rep.qza and taxonomy.qza are available but I cant seem to find the command for rooted-tree.qza


Hello Leah,

I would need a tree expert to ‘qiime-in’ to confirm this, but I don’t think there is a recommended way to build a ‘supertree’ in Qiime 2 right now… :cry: :deciduous_tree:

But don’t worry, I have a workaround!

Once you have merged your feature sequences in rep.qza, you could use that to build a new tree with your program of choice.
:deciduous_tree: :smile: :palm_tree:


@wasade, got any tip about trees? Do you think SEPP would work for Leah?

Hey @colinbrislawn and @kedi,

I’m not aware of an implementation to merge fragment insertion trees that result from SEPP together. The easiest thing would be as @colinbrislawn suggests which is to take the merged FeatureData[Sequence] qza, and rerun fragment insertion.

Similarly, I’m not aware of a defensible means to merge de novo trees. If that is needed, I strongly advise re-aligning and reconstructing the tree. If using de novo trees, then I also advise a review of the SEPP benchmarking paper as it highlights a few potential concerns with de novo trees.

All the best,


Thanks for your prompt response, I merged the rep.qza : )



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