About
Introduction
What is Nextstrain?
Parts of a whole
Augur → Auspice
Interpreting analyses
Phylogenetic trees
Phylogeographic map
Interaction
Pathogens
Nextstrain Groups
Tutorials
Installing
Running a phylogenetic workflow
Creating a phylogenetic workflow
Exploring SARS-CoV-2 evolution
Creating a bacterial phylogenetic workflow
Writing a narrative
Analyzing genomes with Nextclade
Using a pathogen repository
Running an ingest workflow
Creating a pathogen repository
Creating an ingest workflow
How-to Guides
Bioinformatics
Filtering and Subsampling
Augur and snakemake
Missing sequence data (gaps, indels, ambiguity)
Finding a
translate
and
align
reference file
Importing BEAST MCC trees into augur
Manually Labeling Clades on a Nextstrain Tree
Adding Custom Trait Colors
Adding Custom Lat-Long Data
Using VCF Input
Using Fasta Input
Inferring Sequence Traits (like Drug Resistance)
Examples of Augur in the wild
Sharing analyses
Nextstrain Groups
Customize your page
Nextstrain Community
Public URLs
SARS-CoV-2 datasets
Downloading data
Communicating scientific insights
Communicating Results Using Narratives
Converting a narrative to PDF
Viewing previous analyses
Managing an installation
Contributing
Components
Augur
Auspice
Nextstrain CLI
Nextclade CLI
nextstrain.org
Reference
Glossary
Data formats
Data files
FAQ
Snakemake style guide
Documentation style guide
Governance
Nextstrain
Home
Edit on GitHub
Index
A
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B
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C
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D
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E
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I
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J
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N
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O
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P
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R
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V
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W
A
Augur
Auspice
B
build
(verb)
build step
C
Community Contributors
core repository
Core Team
core workflow
D
dataset
E
Editors
I
ingest dataset
ingest workflow
J
JSONs
N
narrative
Nextclade dataset
Nextclade workflow
Nextstrain CLI
O
Owners
P
pathogen repository
phylogenetic dataset
phylogenetic workflow
Private
Project Leads
Public
R
runtime
V
Viewers
W
workflow
Read the Docs
v: latest
Versions
latest
Downloads
On Read the Docs
Project Home
Builds