QIIME™ has been succeeded by QIIME 2™
As of 1 January 2018, QIIME 2 has succeeded QIIME 1. Refer to https://qiime2.org to learn how to install and start using QIIME 2.
QIIME 1 is no longer officially supported; development and support efforts are focused entirely on QIIME 2. Background on the transition is here.
If you're just getting started with QIIME, you should learn QIIME 2, not QIIME 1. QIIME 1 is outdated, and QIIME 2 contains many improvements to analytic functionality, is easier to install, and is easier to use.
Citing QIIME 2? If you used QIIME 2 in your work, cite Bolyen E, Rideout JR, Dillon MR, Bokulich, NA, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology. 2019;37(8):852-857. DOI: 10.1038/s41587-019-0209-9.
Where to find QIIME 1 archives
The original QIIME 1 source code, full repository history, and documentation website are preserved across three independent public archives. The sections below are organized by what you're looking for.
Looking to cite QIIME 1?
Cite the QIIME 1 publication in Nature Methods:
- Caporaso JG, Kuczynski J, Stombaugh J, et al. QIIME allows analysis of high-throughput community sequencing data. Nature Methods. 2010;7(5):335-336. DOI: 10.1038/nmeth.f.303
Looking for the QIIME 1 source code (release 1.9.1)?
The official archived release is on Zenodo with a permanent DOI:
- DOI: 10.5281/zenodo.18036
- Contents:
qiime-1.9.1.zip— full source tarball including theqiime/Python package,scripts/,tests/,examples/,doc/(Sphinx source for the documentation),COPYING.txt, andChangeLog.md.
Looking for the full git history of QIIME 1?
The biocore/qiime repository — including all releases (1.3.0 through 1.9.1), tags, branches, the full commit history from 2009 through the final commit in January 2018, and post-1.9.1 documentation updates that were never tagged as a release — is preserved by Software Heritage:
- Archive page: archive.softwareheritage.org → biocore/qiime
- Each commit has a permanent SWHID identifier that can be cited directly. Use this when you need to reference a specific commit, examine history, or verify provenance.
Looking for the QIIME 1 documentation website as it appeared at qiime.org?
The Internet Archive's Wayback Machine has captures of the live site spanning multiple years:
- web.archive.org → qiime.org
- Use this to browse the documentation, tutorials, install instructions, and version-specific docs as they were originally rendered. The underlying Sphinx source for the same content is in
doc/within the Zenodo deposit and the Software Heritage archive.
The successor project, QIIME 2, is at https://qiime2.org and is actively maintained.