# Why has GNEISS been deprecated from Qiime2?
**URL:** https://forum.qiime2.org/t/why-has-gneiss-been-deprecated-from-qiime2/18333
**Category:** User Support
**Tags:** gneiss, r
**Created:** [February 1, 2021, 9:05pm UTC](https://forum.qiime2.org/t/why-has-gneiss-been-deprecated-from-qiime2/18333 "2021-02-01T21:05:28Z")
**Posts on this page:** 6
**Page:** 1
### Author:  [@ecg](https://forum.qiime2.org/u/ecg)
#### Post date: [February 1, 2021, 9:05pm UTC](https://forum.qiime2.org/t/why-has-gneiss-been-deprecated-from-qiime2/18333/1 "2021-02-01T21:05:28Z")
I am trying to re-run an analysis I had from a couple of years ago, and I see [Differential abundance analysis with gneiss — QIIME 2 2020.11.1 documentation](https://docs.qiime2.org/2020.11/tutorials/gneiss/) that gneiss has been deprecated in the newer version of QIIME, why is this? and if I'd like to run gneiss on R, how can I import my gneiss\_hierarchy.qza and gneiss\_heatmap.qzv into R?
Thanks,
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### Author:  [@mortonjt](https://forum.qiime2.org/u/mortonjt)
#### Post date: [February 2, 2021, 4:51am UTC](https://forum.qiime2.org/t/why-has-gneiss-been-deprecated-from-qiime2/18333/3 "2021-02-02T04:51:31Z")
Hi @ecg, thank you for your interest in gneiss.
Gneiss has not been deprecated -- only some of the visualizers have been deprecated in favor of Empress. By the next release, there will be compatibility between Songbird (possibly Aldex2) and Gneiss, where the ILR transform can be applied directly to differential abundance analysis results.
Of course, there will be more features coming up in the future (hence the [FeatureTensor](https://forum.qiime2.org/t/thoughts-on-differential-and-tensor-types/18210/7) discussion)
See the following pull requests.
>
>
> This is a jupyter notebook running the ILR transform analysis on the folivores d…ataset. Below is a screenshot, with taxonomies highlighted on the tips and the balance labels highlighted on the branches, identifying the dietary split between the monkey samples.
>
> !\[image\](https://user-images.githubusercontent.com/4184797/97658094-14d2a180-1a31-11eb-8429-0387f6324c5e.png)
>
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> This is addressing #70 , outputting an ordination results object containing ILR …coordinates.
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> CC @ElDeveloper , @fedarko
Regarding your questions
1. gneiss\_hierarchy.qza can export a newick file, which can be read into R. See [Exporting data — QIIME 2 2019.10.0 documentation](https://docs.qiime2.org/2019.10/tutorials/exporting/#exporting-a-phylogenetic-tree)
2. gneiss\_heatmap.qzv, this probably can't be ported into R, but there are a number of tools that support phylogenetic heatmaps in R. See for instance [phylo.heatmap: Creates a phylogenetic heat map in phytools: Phylogenetic Tools for Comparative Biology (and Other Things)](https://rdrr.io/cran/phytools/man/phylo.heatmap.html)
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### Author:  [@TurboQiimer](https://forum.qiime2.org/u/TurboQiimer)
#### Post date: [February 2, 2021, 2:46pm UTC](https://forum.qiime2.org/t/why-has-gneiss-been-deprecated-from-qiime2/18333/4 "2021-02-02T14:46:49Z")
Hi @mortonjt
Is GNEISS alternative software for ANCOM? Am I right? And among the different [GNEISS methods](https://docs.qiime2.org/2020.11/plugins/available/gneiss/), which one is widely used and which one do you suggest?
Thanks
Qiimer
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### Author:  [@Mechah](https://forum.qiime2.org/u/Mechah)
#### Post date: [February 5, 2021, 10:25am UTC](https://forum.qiime2.org/t/why-has-gneiss-been-deprecated-from-qiime2/18333/5 "2021-02-05T10:25:00Z")
> [@mortonjt](#):
>
> By the next release, there will be compatibility between Songbird (possibly Aldex2) and Gneiss, where the ILR transform can be applied directly to differential abundance analysis results.
Awesome, thanks! 🙂
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### Author:  [@ecg](https://forum.qiime2.org/u/ecg)
#### Post date: [February 5, 2021, 11:09am UTC](https://forum.qiime2.org/t/why-has-gneiss-been-deprecated-from-qiime2/18333/6 "2021-02-05T11:09:54Z")
Looking forward to the next version! Thanks @mortonjt
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### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [March 8, 2021, 5:09pm UTC](https://forum.qiime2.org/t/why-has-gneiss-been-deprecated-from-qiime2/18333/7 "2021-03-08T17:09:59Z")
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