flu-crew / octoFLULinks
Script that labels phylogenetic clades based on the clade of the nearest neighbor using patristic distances determined from the tree.
☆11Updated 10 months ago
Alternatives and similar repositories for octoFLU
Users that are interested in octoFLU are comparing it to the libraries listed below
Sorting:
- Simple Manipulation Of Trees☆13Updated last month
- AMR/VF LGT focused bacterial genomics analysis workflow☆27Updated 6 months ago
- Collection of R scripts for SARS-CoV-2 (variant) analyses☆12Updated 2 years ago
- This RAPT repository has been retired as of December 2024. NCBI's Read assembly and Annotation Pipeline Tool (RAPT) was a pilot service.☆58Updated 6 months ago
- Virus reassortment inference software. Infers both recent and ancestral reassortment and uses flexible molecular clock constraints.☆17Updated 2 weeks ago
- Influenza data pipeline to automate genotyping assignment☆37Updated 4 months ago
- A listing of software, tools and databases useful for virome analysis☆46Updated this week
- Influenza genome analysis Nextflow workflow☆28Updated 3 weeks ago
- Phylogenetic maximum representation sampling: choosing most representative strains or taxa☆39Updated 2 weeks ago
- An `R` package for various phylogenetic and evolutionary biology data manipulations☆12Updated 7 years ago
- map Illumina metagenomes to genomes!☆38Updated last month
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆50Updated 3 years ago
- Extract metadata from biosamples in NCBI☆16Updated 4 years ago
- Influenza genome analysis Nextflow workflow☆23Updated 3 weeks ago
- ☆10Updated 4 months ago
- Nextstrain build for avian influenza viruses☆27Updated last week
- Java software to analyse phylogeny-trait correlations in discrete traits, accounting for phylogenetic uncertainty via posterior sampling.☆12Updated 8 years ago
- A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data☆66Updated 3 years ago
- High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers☆43Updated last year
- Assembling the cause of phenotypes and genotypes from NGS data☆29Updated 5 years ago
- ☆45Updated 2 years ago
- Inference of putative transmission phylogenetic clusters☆11Updated 5 years ago
- TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…☆56Updated last week
- VIGOR4☆21Updated last month
- Remove contaminated contigs from genomes using k-mers and taxonomies.☆59Updated last year
- 🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes☆80Updated 2 months ago
- MAG Circularization Method☆32Updated 3 years ago
- PLSDB pipeline to collect bacterial plasmids from NCBI☆38Updated 11 months ago
- Strain Resolution ON Graphs☆47Updated 2 years ago
- Pipeline for analysing intergenic regions in bacteria☆40Updated 5 years ago