Table of contents
Nextstrain Documentation
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
SARS-CoV-2
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
Zika Tutorial
Zika tutorial – fasta input
MTb tutorials using vcf data
Writing a Narrative
How-to Guides
Installing Nextstrain
Local Installation
Nextstrain CLI installation
Augur Installation
Auspice Installation
Help! I’m using Windows
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 builds
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
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Interpreting Nextstrain
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Interpreting Nextstrain
¶
Learn how to interpret Nextstrain analyses.
Table of contents
How to interpret the phylogenetic trees
Interacting with Nextstrain’s phylogeographic visualisations
Interpreting the Map
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