Tools for analyzing and comparing SARS-CoV-2 phylogenies
☆10Nov 21, 2020Updated 5 years ago
Alternatives and similar repositories for strain_phylogenetics
Users that are interested in strain_phylogenetics are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Munge GenBank files into FASTA and tab-separated metadata☆15Feb 5, 2026Updated 2 months ago
- SARs-CoV-2 Primer schemes☆16May 14, 2025Updated 11 months ago
- Nanopore read de-multiplexer☆13Mar 25, 2020Updated 6 years ago
- 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
- VGEA (Viral Genomes Easily Analyzed) is a pipeline for analysis of RNA virus next-generation sequencing data.☆20Sep 12, 2021Updated 4 years ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Splitting and accelerating the Oxford Nanopore basecaller guppy using CPU with the SLURM job scheduler☆16Jul 1, 2024Updated last year
- ☆51Mar 11, 2022Updated 4 years ago
- ☆21Apr 2, 2025Updated last year
- Store of the trained model for pangolin to access.☆55Oct 4, 2022Updated 3 years ago
- Reference-guided multiple sequence alignment of viral genomes☆71Nov 6, 2025Updated 5 months ago
- Ultrafast Sample Placement on Existing Trees☆140Feb 6, 2026Updated 2 months ago
- Renders SVG schema of SARS-CoV-2 clade as defined by Nextstrain☆17Nov 24, 2025Updated 4 months ago
- ☆25Jun 25, 2024Updated last year
- Primer schemes for real-time genome epidemiology☆30Jun 14, 2023Updated 2 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- ☆11Aug 18, 2024Updated last year
- The Zika bioinformatics pipeline☆37Mar 29, 2020Updated 6 years ago
- Tool for analysing viral diversity from High Throughput Sequencing☆12Nov 20, 2025Updated 4 months ago
- This repository houses the code to run SURPI+, a rapid computational pipeline for comprehensive identification of pathogens from clinical…☆42Nov 20, 2019Updated 6 years 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…☆37Updated this week
- Small collection of tools for performing quality control on coronavirus sequencing data and genomes☆49Apr 25, 2024Updated last year
- Sequence simulator☆55Feb 3, 2025Updated last year
- Phylogenetic tree library for JavaScript/Node.js☆39Nov 16, 2022Updated 3 years ago
- Programmatically interact with the GISAID database.☆80Aug 5, 2025Updated 8 months ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Screening Historical Events of Recombination in a Phylogeny via Ancestral Sequences☆11Sep 3, 2025Updated 7 months ago
- ☆13Nov 26, 2025Updated 4 months ago
- A simulator for horizontal gene transfer (HGT) in microbial communities☆10Oct 5, 2020Updated 5 years ago
- Accurate, resource-frugal and deterministic DNA sequence classifier.☆36Mar 4, 2026Updated last month
- CRISPR/Cas-directed HDR genome editing suite: finds+scores gRNA targets, generates donor DNAs, & produces optimal cPCR primer designs.☆13Oct 18, 2021Updated 4 years ago
- Vials is a Caleydo Web application for visualizing alternative splicing based on mRNAseq data.☆13Jan 8, 2018Updated 8 years ago
- Docker image build for nextstrain/base☆12Mar 19, 2026Updated 3 weeks ago
- Workflow for SARS-CoV-2 genome Assembly at FioCruz/IAM☆29Feb 6, 2024Updated 2 years ago
- Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequenc…☆37Jul 11, 2025Updated 9 months ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- ☆38Jan 12, 2026Updated 3 months 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
- ☆21Feb 12, 2026Updated 2 months ago
- Detection of viruses from RNA-Seq on human samples☆46Mar 18, 2023Updated 3 years ago
- Indel-aware consensus for aligned BAM☆21Aug 16, 2025Updated 8 months ago
- ☆13Aug 20, 2025Updated 7 months ago
- For when you just need a coverage plot.☆11Mar 26, 2021Updated 5 years ago