merge rooted.qza trees

[kedi (Leah)]

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

Thanks

[colinbrislawn (Colin J Brislawn)]

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...

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.

Colin

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

[wasade (Daniel McDonald)]

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,
Daniel

[kedi (Leah)]

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

Regards