Table of contents
Nextstrain Documentation
Install Nextstrain
Learn
About Nextstrain
Interpreting Nextstrain
How to interpret the phylogenetic trees
Interacting with Nextstrain’s phylogeographic visualisations
Interpreting the Map
Pathogens
Coronavirus
COVID-19 Frequently Asked Questions
SARS-CoV-2
Technical FAQs
Human CoV
Tutorials
Quickstart
Explore Zika virus evolution
Explore Tuberculosis evolution
Explore SARS-CoV-2 evolution
A Getting Started Guide to the Genomic Epidemiology of SARS-CoV-2
Setup and installation
Preparing your data
Orientation: so, what does Nextstrain
do
?
Overview of this repository (i.e., what do these files do?)
Running the analysis
Customizing analysis
Customizing your Auspice visualization
Clade Naming & Definitions
Visualizing and sharing results
Guidance for interpretation
Nextstrain Narratives
Writing a Narrative
How-to Guides
Running Bioinformatic Analyses
Manually Labeling Clades on a Nextstrain Tree
Augur and snakemake
Finding a
translate
and
align
reference file
Importing BEAST MCC trees into augur
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 through Nextstrain
Scalable Sharing with Nextstrain Groups
Community Sharing of Results Via GitHub
Fetch datasets & narratives accessible via a public URL
Add your dataset to the collection of SARS-CoV-2 datasets
Download data
Communicating scientific insights
Communicating Results Using Narratives
Converting a narrative to PDF
Contributing to Nextstrain
Nextstrain Github Contributing Guide
Contributing to Documentation
Contribute to Nextstrain CLI
Contribute to Augur
Contribute to Auspice
Reference Guides
Data formats of Nextstrain
Data Formats Used by Nextstrain
Augur: A bioinformatics toolkit for phylogenetic analysis
Auspice: An Open-source Interactive Tool for Visualising Phylogenomic Data
Nextstrain command-line interface (CLI)
Nextstrain
Docs
»
Tutorials
Edit on GitHub
Tutorials
¶
Tutorials to help you get started with Nextstrain!
Table of contents
Quickstart
Explore Zika virus evolution
Explore Tuberculosis evolution
Explore SARS-CoV-2 evolution
Writing a Narrative
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