Bulding a phylogeny using taxonomy

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Hi, a question as a pretty new user of QIIME2 (and a researcher in the microbiome world).

I'm working with a collabrator, and recived from him, after he DADA2 processed it, table containing the observed ASV's per sample , and a table with the taxonomic assignment per observed ASV created using a refrence database, which I will import as (FeatureTable[Frequency]) and (FeatureData[Taxonomy]), respectively.

After going through the phylogeny pipeline I noticed you have to provide a FeatureData[Sequence] artifact. is there any way to generate the phylogeny tree using the taxonomic data I have?

Thanks a lot

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Hi @Omer,

The only way to make a phylogeny is through the use of character state information, e.g. molecular sequences, morphology, etc... .

Are you asking for a way to visualize your taxonomic information as hierarchy tree? If so, this is currently not possible within QIIME 2. I think there might be external tools to do this.

Also note, that phylogeny and taxonomy often do not agree with one another. What you may observe through a taxonomy tree may not be the same as what you generate from a phylogenetic tree, for a variety of reasons.

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ok thanks. So in this case it means I have to get the upstream sequences after the DADA2 process?

[/quote]
Also note, that phylogeny and taxonomy often do not agree with one another. What you may observe through a taxonomy tree may not be the same as what you generate from a phylogenetic tree, for a variety of reasons.
[/quote]

Could you please expend on that point?

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Yes. Although you can construct a phylogeny with these data. It is often recommended that you perform additional filtering of the data after denoising. See the following tutorial for some examples:

Note: make sure the dop menu at the top of these pages is set to:
Command Line (q2cli)

You can also find some examples in the other QIIME 2 tutorials.

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thanks again. what is the qiime2 pipline for consructing a phylogeny using these data? I have found only using FeatureData[Sequence] as an artifact.

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Everything you need to learn how to run QIIME 2 is on the Tutorials page. Specifically, read through the Phylogeny tutorial, and the associated YouTube videos:

Good Luck!

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