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3.28.0
Installation and usage
| 📚 Docs | docs.nextstrain.org/projects/nextclade | ||||||||
| 🌍 Web | clades.nextstrain.org | ||||||||
| 📥 CLI |
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| 🐋 Docker | docker pull nextstrain/nextclade:3.28.0 (tags) | ||||||||
| 🐍 Conda | conda install -c bioconda nextclade=3.28.0 (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
Nextclade Web: results table
- Style of the tree colors of clades: Settings > Tree sets how the results table shows the tree colors of clades and clade-like values, such as the Pango lineage: as a circle before the value, as before, as a pale badge with a border in the tree color, or not at all. The text of a badge stays dark on every tree color, so that it stays legible. A click on a circle or on a badge shows the value on the tree. The tooltips of the circles and badges say where to change the style. See #1843
- Separate zoom settings: the tree button of a sequence name and the circle or badge of a clade have separate settings for whether a click zooms the tree, because one selects a sequence and the other filters the tree to many sequences. The tree buttons keep your current setting, and the clade buttons start with the tree keeping its zoom. See #1843
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