# Combining 16S (V4) and shotgun on one Greengenes2 tree for UniFrac — namespace mismatch (2024.09)
**URL:** https://forum.qiime2.org/t/combining-16s-v4-and-shotgun-on-one-greengenes2-tree-for-unifrac-namespace-mismatch-2024-09/34285
**Category:** Library Support
**Tags:** greengenes2
**Created:** [August 11, 2026, 9:53pm UTC](https://forum.qiime2.org/t/combining-16s-v4-and-shotgun-on-one-greengenes2-tree-for-unifrac-namespace-mismatch-2024-09/34285 "2026-08-11T21:53:25Z")
**Posts on this page:** 4
**Page:** 1
### Author:  [@dbadri](https://forum.qiime2.org/u/dbadri)
#### Post date: [August 11, 2026, 9:53pm UTC](https://forum.qiime2.org/t/combining-16s-v4-and-shotgun-on-one-greengenes2-tree-for-unifrac-namespace-mismatch-2024-09/34285/1 "2026-08-11T21:53:25Z")
Hello!
I am computing UniFrac across paired 16S (V4) and shotgun metagenomic data on the shared Greengenes2 phylogeny and I have ended up with three different feature ID namespaces that I can't get onto a single tree. I would appreciate guidance on which namespace the combined analysis should live in and how to convert into it.
What I have:
- **16S table (md5).** My V4 reads were paired end merged, so I denoised forward only and truncated to 150 nt to match the placed fragments. `qiime greengenes2 filter-features` against `2024.09.taxonomy.md5.nwk.qza` then retained 100% of features. The resulting FeatureTable has **md5** feature IDs.
- **Shotgun table (GG2 record IDs).** Woltka/WoL2 genome IDs translated to Greengenes2 IDs (`G...`, `GB-GCA-...`, `RS-GCF-...`) via the WoL2--\>GG2 crosswalk (`wol2gg.tsv` from the [WoL2 release](https://ftp.microbio.me/pub/wol2/taxonomy/gg2/)).
- **Pruned tree (asv namespace).** Pruned from `2024.09.phylogeny.asv.nwk.qza`, so its tips are ASV sequences with genome IDs for backbone records.
So the tree is asv-namespace, the 16S table is md5 and the shotgun side is record IDs—three namespaces and my 16S features are consequently not tips in the tree so cross platform UniFrac comes out empty.
Questions:
1. For a combined 16S + shotgun UniFrac analysis, which namespace is the intended target and how do I get all three inputs into it?
2. Is there a supported way to relabel an md5 `filter-features` table to record IDs (or ASV/sequence IDs) for 2024.09? `qiime greengenes2 relabel` requires a `ReferenceMap` artifact,
[asv-table-gg2-v4.qza](https://forum.qiime2.org/uploads/short-url/v88EqwlOnioQtC8mr7m9uMO4hUM.qza) (45.9 KB)
[asv-seqs-filtered.qza](https://forum.qiime2.org/uploads/short-url/yKR3OyZ8touh5vHGWSSMHZ6w1WN.qza) (45.0 KB)
Attached: my md5 16S feature table and the corresponding rep-seqs. Happy to provide the shotgun table or crosswalk if useful. Thanks!
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### Author:  [@wasade](https://forum.qiime2.org/u/wasade)
#### Post date: [August 13, 2026, 6:28pm UTC](https://forum.qiime2.org/t/combining-16s-v4-and-shotgun-on-one-greengenes2-tree-for-unifrac-namespace-mismatch-2024-09/34285/4 "2026-08-13T18:28:08Z")
Hi @dbadri,
If the 16S are using MD5s then the phylogeny needs to use the MD5 variant not the ASV one. The trees are the same, but the labels on the tips differ from whether they use MD5 or the ASV sequence for the tip names; the genome IDs in the tree are unaffected. I don't know what the crosswalk is that's referenced, but the genome IDs used in the phylogeny are the same ID structure in WoL2 (e.g., G#########)
Best,
Daniel
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### Author:  [@dbadri](https://forum.qiime2.org/u/dbadri)
#### Post date: [August 19, 2026, 2:26pm UTC](https://forum.qiime2.org/t/combining-16s-v4-and-shotgun-on-one-greengenes2-tree-for-unifrac-namespace-mismatch-2024-09/34285/5 "2026-08-19T14:26:58Z")
I downloaded the MD5 tree and it solved the problem. Thank you!
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### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [September 19, 2026, 8:27pm UTC](https://forum.qiime2.org/t/combining-16s-v4-and-shotgun-on-one-greengenes2-tree-for-unifrac-namespace-mismatch-2024-09/34285/6 "2026-09-19T20:27:35Z")
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