Pipeline components for real-time phylodynamic analysis
☆275Updated this week
Alternatives and similar repositories for augur
Users that are interested in augur are comparing it to the libraries listed below
Sorting:
- Web app for visualizing pathogen evolution☆305Jan 21, 2026Updated last month
- RethinkDB database to support real-time virus analysis☆35Feb 19, 2026Updated last week
- Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction☆249Updated this week
- Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement☆250Feb 5, 2026Updated 3 weeks ago
- Nextstrain build for SARS-CoV-2☆1,359Jan 31, 2026Updated last month
- Store of the trained model for pangolin to access.☆55Oct 4, 2022Updated 3 years ago
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Aug 14, 2023Updated 2 years ago
- Ultrafast Sample Placement on Existing Trees☆139Feb 6, 2026Updated 3 weeks ago
- The Nextstrain command-line interface (CLI)—a program called nextstrain—which aims to provide a consistent way to run and visualize patho…☆28Feb 19, 2026Updated last week
- viral-ngs: complete pipelines☆73Updated this week
- Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input…☆36May 1, 2022Updated 3 years ago
- Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation☆114Updated this week
- SARs-CoV-2 Primer schemes☆16May 14, 2025Updated 9 months ago
- Northern Arizona SNP Pipeline☆20Oct 29, 2024Updated last year
- Real-time tracking of influenza evolution☆88Sep 8, 2023Updated 2 years ago
- A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.☆349Apr 12, 2023Updated 2 years ago
- iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.☆134Feb 22, 2026Updated last week
- baltic - adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. This fork will no longe…☆12Dec 18, 2019Updated 6 years ago
- Software package for assigning SARS-CoV-2 genome sequences to global lineages.☆447Feb 19, 2026Updated last week
- INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomi…☆41Updated this week
- The Nextstrain website☆96Updated this week
- Inferring spatiotemporal dynamics of the H1N1 influenza pandemic from sequence data☆33Oct 25, 2013Updated 12 years ago
- VIGOR4☆21Aug 15, 2025Updated 6 months ago
- A pipeline that ingests SARS-CoV-2 (i.e. nCoV) data from GISAID and Genbank, transforms it, stores it on S3, and triggers Nextstrain nCoV…☆37Feb 4, 2026Updated 3 weeks ago
- The ARTIC fieldbioinformatics pipeline☆129Jan 7, 2026Updated last month
- Bayesian Evolutionary Analysis Sampling Trees☆235Updated this week
- Virus reassortment inference software. Infers both recent and ancestral reassortment and uses flexible molecular clock constraints.☆22Sep 29, 2025Updated 5 months ago
- Programmatically interact with the GISAID database.☆80Aug 5, 2025Updated 6 months ago
- serious constellations of reoccurring phylogenetically-independent origin☆39Feb 13, 2026Updated 2 weeks ago
- ☆27Aug 2, 2023Updated 2 years ago
- Influenza data pipeline to automate genotyping assignment☆39Oct 14, 2025Updated 4 months ago
- Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…☆42Aug 5, 2024Updated last year
- Reference-guided multiple sequence alignment of viral genomes☆70Nov 6, 2025Updated 3 months ago
- The Zika bioinformatics pipeline☆36Mar 29, 2020Updated 5 years ago
- A tool for exploring large trees in the browser☆123Feb 4, 2026Updated 3 weeks ago
- A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), wit…☆91Nov 8, 2023Updated 2 years ago
- Fast viral consensus genome reconstruction☆25Feb 5, 2026Updated 3 weeks ago
- Nextstrain build for dengue virus☆13Dec 16, 2025Updated 2 months ago
- Tools for analyzing and comparing SARS-CoV-2 phylogenies☆10Nov 21, 2020Updated 5 years ago