# merge rooted.qza trees

**URL:** https://forum.qiime2.org/t/merge-rooted-qza-trees/13726
**Category:** User Support
**Tags:** feature-classifier
**Created:** [February 21, 2020, 8:18pm UTC](https://forum.qiime2.org/t/merge-rooted-qza-trees/13726 "2020-02-21T20:18:36Z")
**Posts on this page:** 5
**Page:** 1

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### Author: ![kedi](https://forum.qiime2.org/user_avatar/forum.qiime2.org/kedi/32/7272_2.png) [@kedi](https://forum.qiime2.org/u/kedi)
#### Post date: [February 21, 2020, 8:18pm UTC](https://forum.qiime2.org/t/merge-rooted-qza-trees/13726/1 "2020-02-21T20:18:36Z")

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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

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### Author: ![colinbrislawn](https://forum.qiime2.org/user_avatar/forum.qiime2.org/colinbrislawn/32/6221_2.png) [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [February 24, 2020, 12:06am UTC](https://forum.qiime2.org/t/merge-rooted-qza-trees/13726/2 "2020-02-24T00:06:12Z")

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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?

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### Author: ![wasade](https://forum.qiime2.org/user_avatar/forum.qiime2.org/wasade/32/2317_2.png) [@wasade](https://forum.qiime2.org/u/wasade)
#### Post date: [February 24, 2020, 9:17pm UTC](https://forum.qiime2.org/t/merge-rooted-qza-trees/13726/3 "2020-02-24T21:17:20Z")

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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](https://msystems.asm.org/content/3/3/e00021-18) as it highlights a few potential concerns with _de novo_ trees.

All the best,  
Daniel

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### Author: ![kedi](https://forum.qiime2.org/user_avatar/forum.qiime2.org/kedi/32/7272_2.png) [@kedi](https://forum.qiime2.org/u/kedi)
#### Post date: [February 25, 2020, 3:35pm UTC](https://forum.qiime2.org/t/merge-rooted-qza-trees/13726/4 "2020-02-25T15:35:38Z")

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

Regards

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### Author: ![system](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/1/21af5fe23cb6f4579467c66a9ed94e55274ca7bd.svg) [@system](https://forum.qiime2.org/u/system)
#### Post date: [March 27, 2020, 9:35pm UTC](https://forum.qiime2.org/t/merge-rooted-qza-trees/13726/5 "2020-03-27T21:35:40Z")

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