Skip to content

Navigation Menu

Appearance settings

nextstrain

GitHub Copilot
Write better code with AI

GitHub Spark New
Build and deploy intelligent apps

GitHub Models New
Manage and compare prompts

GitHub Advanced Security
Find and fix vulnerabilities

Actions
Automate any workflow
Codespaces
Instant dev environments

Issues
Plan and track work

Code Review
Manage code changes

Discussions
Collaborate outside of code

Code Search
Find more, search less
Explore

Why GitHub

Documentation

GitHub Skills

Blog
Integrations

GitHub Marketplace

MCP Registry
View all features
By company size

Enterprises

Small and medium teams

Startups

Nonprofits
By use case

App Modernization

DevSecOps

DevOps

CI/CD

View all use cases
By industry

Healthcare

Financial services

Manufacturing

Government

View all industries
View all solutions
Topics

AI

DevOps

Security

Software Development

View all
Explore

Learning Pathways

Events & Webinars

Ebooks & Whitepapers

Customer Stories

Partners

Executive Insights
GitHub Sponsors
Fund open source developers
The ReadME Project
GitHub community articles
Repositories

Topics

Trending

Collections
Enterprise platform
AI-powered developer platform
Available add-ons

GitHub Advanced Security
Enterprise-grade security features

Copilot for business
Enterprise-grade AI features

Premium Support
Enterprise-grade 24/7 support
Pricing

Search code, repositories, users, issues, pull requests...

Search

Clear

Search syntax tips

Provide feedback

We read every piece of feedback, and take your input very seriously.

Include my email address so I can be contacted

Saved searches

Use saved searches to filter your results more quickly

Name

Query

To see all available qualifiers, see our documentation.

Appearance settings

You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session.

Dismiss alert

Nextstrain

Real-time tracking of pathogen evolution

208 followers
https://nextstrain.org
@nextstrain
@[email protected]

Overview
Repositories
Projects
Packages
People

More

Overview
Repositories
Projects
Packages
People

Pinned Loading

ncov ncov Public

Nextstrain build for SARS-CoV-2

Python 1.4k 406
augur augur Public

Pipeline components for real-time phylodynamic analysis

Python 275 136
auspice auspice Public

Web app for visualizing pathogen evolution

JavaScript 304 169

Repositories

Loading

Type

Select type

All Public Sources Forks Archived Mirrors Templates

Language

Select language

All C Dockerfile Go HTML JavaScript Jupyter Notebook Makefile Nextflow Perl Python R Rust Shell TeX TypeScript WDL

Sort

Select order

Last updated Name Stars

Showing 10 of 100 repositories

ncov Public
Nextstrain build for SARS-CoV-2

nextstrain/ncov’s past year of commit activity

Python 1,353 MIT 406 73 22 Updated Oct 24, 2025
nextstrain.org Public
The Nextstrain website

nextstrain/nextstrain.org’s past year of commit activity

JavaScript 97 AGPL-3.0 52 76 12 Updated Oct 24, 2025
norovirus Public

nextstrain/norovirus’s past year of commit activity

Python 2 MIT 0 8 1 Updated Oct 24, 2025
forecasts-ncov Public
SARS-CoV-2 variant growth rates and frequency forecasts

nextstrain/forecasts-ncov’s past year of commit activity

Python 8 3 13 5 Updated Oct 23, 2025
variant-nowcast-hub Public Forked from reichlab/variant-nowcast-hub
A repository to store COVID-19 variant nowcasts collected as a modeling hub.

nextstrain/variant-nowcast-hub’s past year of commit activity

R 0 MIT 15 0 0 Updated Oct 23, 2025
forecasts-flu Public
Seasonal influenza variant growth rates and frequency forecasts

nextstrain/forecasts-flu’s past year of commit activity

Python 1 MIT 0 3 1 Updated Oct 23, 2025
seasonal-flu Public
Scripts. config, and snakefiles for seasonal-flu nextstrain builds

nextstrain/seasonal-flu’s past year of commit activity

Python 53 28 27 7 Updated Oct 23, 2025
measles Public
Nextstrain build for measles virus

nextstrain/measles’s past year of commit activity

Python 3 8 4 7 Updated Oct 23, 2025
lassa Public
Nextstrain build for Lassa virus

nextstrain/lassa’s past year of commit activity

Python 1 5 10 2 Updated Oct 23, 2025
infra Public
Nextstrain shared infrastructure

nextstrain/infra’s past year of commit activity

Makefile 0 0 2 1 Updated Oct 23, 2025

View all repositories

People

Top languages

Loading…

Uh oh!

There was an error while loading. Please reload this page.

Most used topics

Loading…

Uh oh!

There was an error while loading. Please reload this page.

Footer

© 2025 GitHub, Inc.

Footer navigation

Terms
Privacy
Security
Status
Community
Docs
Contact

You can’t perform that action at this time.