# How to make a Cladogram with QIIME 2 data?
**URL:** https://forum.qiime2.org/t/how-to-make-a-cladogram-with-qiime-2-data/24366
**Category:** Other Bioinformatics Tools
**Tags:** dokdo, lefse
**Created:** [October 6, 2022, 10:09pm UTC](https://forum.qiime2.org/t/how-to-make-a-cladogram-with-qiime-2-data/24366 "2022-10-06T22:09:40Z")
**Posts on this page:** 4
**Page:** 1
### Author:  [@Jacob95](https://forum.qiime2.org/u/Jacob95)
#### Post date: [October 6, 2022, 10:09pm UTC](https://forum.qiime2.org/t/how-to-make-a-cladogram-with-qiime-2-data/24366/1 "2022-10-06T22:09:40Z")
Hello
I am new to QIIME2.
I just finished the QIIME2 tutorial.
There is one thing that I could not get the correct answer by myself.
I want to make the Cladogram with QIIME 2 data on the LeFSe environment.
I have found several suggestions and I have tried them.
But I could not get the result that I want.
There may be some errors...
Can you walk me through the process of making the data can be used in the LeFSe environment?
FWI, I think below is one of the solutions, but I can't understand how to do it.
1. Are my QIIME 2 data (.qza) compatible with dokdo commands?
2. I am curious about the next step after installing dokdo.
Thank you so much.
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### Author:  [@SoilRotifer](https://forum.qiime2.org/u/SoilRotifer)
#### Post date: [October 7, 2022, 1:55pm UTC](https://forum.qiime2.org/t/how-to-make-a-cladogram-with-qiime-2-data/24366/2 "2022-10-07T13:55:23Z")
Hi @Jacob95, welcome to :qiime2:! Hopefully, we can get you running LEfSe. 🙂
Regarding the post:
> [@Weird cladogram](https://forum.qiime2.org/t/weird-cladogram/23711/6):
>
> Hi @Barandouzi, This looks like LEfSe output. If it is, then this is not a true cladogram, despite name of the function. It is merely a dendrogram based on taxonomic ranks, were each node is a taxonomic level. If you do not have | separating the ranks, then you're only ever going to see this "star" cladogram. Where each tip is a unique full taxonomy string. I'd recommend installing [dokdo](https://dokdo.readthedocs.io/en/latest/readme.html?highlight=install#getting-started) into your QIIME 2 environment and then run the [prepare-lefse](https://dokdo.readthedocs.io/en/latest/dokdo_cli.html#prepare-lefse) command. Then upload to [LEfSe Galaxy](https://huttenhower.sph.harvard.edu/galaxy/).
> [@Jacob95](#):
>
> Are my QIIME 2 data (.qza) compatible with dokdo commands?
If you read the [dokdo documentation](https://dokdo.readthedocs.io/en/latest/readme.html) and the tutorials you'll see that dokdo uses the QIIME 2 API and is intended to be used with QIIME 2.
> [@Jacob95](#):
>
> I am curious about the next step after installing dokdo.
Again, everything you need to know is in the dokdo documentation. Here are the [installation instructions](https://dokdo.readthedocs.io/en/latest/readme.html). Though it is much easier to simply install like this:
> conda activate qiime2-2022.8
> pip install git+https://github.com/sbslee/dokdo
> dokdo --help
Then run the [prepare-lefse](https://dokdo.readthedocs.io/en/latest/dokdo_cli.html#prepare-lefse) command as [described here](https://dokdo.readthedocs.io/en/latest/useful_information.html#lefse).
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### Author:  [@Jacob95](https://forum.qiime2.org/u/Jacob95)
#### Post date: [October 17, 2022, 8:24pm UTC](https://forum.qiime2.org/t/how-to-make-a-cladogram-with-qiime-2-data/24366/3 "2022-10-17T20:24:39Z")
Thank you so much!
It worked.
But the result was slightly different from what I have expected so I will make some measurements on my raw data before re-running LEfSe.
Have a good day!
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### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [November 18, 2022, 2:24am UTC](https://forum.qiime2.org/t/how-to-make-a-cladogram-with-qiime-2-data/24366/4 "2022-11-18T02:24:40Z")
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