Nextclade
Table of contents
Home
Migration to Nextclade v3
Nextclade Web
Getting started
Analysis results table
Phylogenetic tree view
Export
Performance tips
URL parameters
Nextclade CLI
Installation
Standalone download
With Docker
With Conda
Build from source
Usage
Reference
Nextclade datasets
Input files
Sequence data
Reference sequence
Genome annotation
Reference tree
Pathogen configuration
Compression, stdin
Output files
All outputs
Nucleotide alignment
Translations
Analysis results (tabular)
Analysis results (JSON)
Phylogenetic tree
Errors and warnings
Compression, stdout
Algorithm
1. Sequence alignment
2. Translation
3. Phylogenetic placement
4. Clade assignment
5. Mutation calling
6. Quality Control (QC)
7. Detection of PCR primer changes
Nextclade as pango lineage classifier: Methods and Validation
Useful links
Frequently asked questions
Terminology
Developer documentation
Developer guide
macOS: development troubleshooting
Recent changes
Nextclade 3.9.1
Nextclade 3.9.0
Nextclade 3.8.2
Nextclade 3.8.1
Nextclade 3.8.0
Nextclade 3.7.4
Nextclade 3.7.3
Nextclade 3.7.2
Nextclade 3.7.1
Nextclade 3.7.0
Nextclade 3.6.0
Nextclade 3.5.0
Nextclade 3.4.0
Nextclade 3.3.1
Nextclade 3.3.0
Nextclade 3.2.1
Nextclade 3.2.0
Nextclade 3.1.0
Nextclade 3.0.1
Nextclade 3.0.0
Older versions
Nextclade
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Nextclade
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Developer documentation
Documentation for developers and maintainers of Nextclade
Developer guide
macOS: development troubleshooting