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3.25.1
Nextclade CLI: distrust compromised eMudhra certificate authorities
In October 2026 the private keys of several eMudhra intermediate certificate authorities became public, so anyone can issue TLS certificates under them. Nextclade CLI no longer trusts certificates from these intermediates, and no longer trusts the root certificate "emSign ECC Root CA - G3" that cross-signed them. Before this change, an attacker who intercepts the connection could use such a certificate to impersonate the dataset server and serve modified datasets. The incident is tracked as CVE-2026-111943. See emudhra.we-have-a-problem.com for details.
Installation and usage
| 📚 Docs | docs.nextstrain.org/projects/nextclade | ||||||||
| 🌍 Web | clades.nextstrain.org | ||||||||
| 📥 CLI |
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| 🐋 Docker | docker pull nextstrain/nextclade:3.25.1 (tags) | ||||||||
| 🐍 Conda | conda install -c bioconda nextclade=3.25.1 (versions)** | ||||||||
| ⌨️ Source code | github.com/nextstrain/nextclade | ||||||||
| 💾 Datasets | github.com/nextstrain/nextclade_data | ||||||||
| 🚩 Issues | Report bugs, suggest features |
* glibc builds are faster and recommended, but require glibc >= 2.14. musl builds are static, run on older Linux distributions, and are slightly slower
** Bioconda releases need manual approval and can be delayed
*** macOS executables are not signed. See the install guide if macOS refuses to run them
Citation
If you use results obtained with Nextclade in a publication, please cite our paper:
Aksamentov, I., Roemer, C., Hodcroft, E. B., & Neher, R. A., (2021). Nextclade: clade assignment, mutation calling and quality control for viral genomes. Journal of Open Source Software, 6(67), 3773, https://doi.org/10.21105/joss.03773
(bibtex)
Where possible, provide a link to Nextclade Web: https://clades.nextstrain.org