Repository containing a method for automatically identifying pathogen lineages from a phylogeny.
☆17May 19, 2023Updated 2 years ago
Alternatives and similar repositories for autolin
Users that are interested in autolin are comparing it to the libraries listed below
Sorting:
- TreeKnit is a package that infers Ancestral Reassortment Graphs for segmented genomes (typically, human influenza).☆14Feb 18, 2025Updated last year
- Script that labels phylogenetic clades based on the clade of the nearest neighbor using patristic distances determined from the tree.☆15Dec 11, 2024Updated last year
- ☆16Apr 6, 2023Updated 2 years ago
- SC2 variant detection and composition pipeline☆19Jul 14, 2023Updated 2 years ago
- Modification of BayesAss 3.0.4 to allow handling of large SNP datasets☆17Feb 19, 2022Updated 4 years ago
- A nextflow pipeline for polishing CLR assemblies☆18Feb 3, 2023Updated 3 years ago
- A simple pipeline for bacterial assembly and quality control☆16Updated this week
- Main development repository for SpreadGL☆20Sep 30, 2024Updated last year
- ☆17Jul 27, 2023Updated 2 years ago
- Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens☆37Jan 22, 2026Updated last month
- An open-source pathogen sequence database dedicated to equitable sharing, transparent governance, & empowering global public health.☆50Updated this week
- A protein language model for learning the SARS-CoV-2 fitness landscape☆12Apr 22, 2025Updated 10 months ago
- Postprocessing gadgets for output generated by RevBayes☆14Feb 22, 2026Updated last week
- Fast, scalable, accurate and accessible Bayesian phylogenetics☆42Feb 23, 2026Updated last week
- Novo&Stitch is a genome assembly reconciliation tool based on optical map.☆10Oct 21, 2019Updated 6 years ago
- Map query sequences to the assemblies of all pre-June 2023 bacteria (https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.2/) on…☆12May 22, 2024Updated last year
- A Rust-based library for phylogenetic analysis and manipulation☆16Feb 10, 2026Updated 3 weeks ago
- Python tool to reduce size and redundancy of phylogenetic datasets☆49Dec 5, 2025Updated 2 months ago
- Rapidly extract reads from a FASTQ file based on taxonomic classification via Kraken2.☆13Jan 26, 2026Updated last month
- ☆10Jun 9, 2025Updated 8 months ago
- ☆30Mar 6, 2025Updated 11 months ago
- Scalable relaxed clock phylogenetic dating☆28Sep 3, 2025Updated 6 months ago
- Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads☆21Aug 2, 2022Updated 3 years ago
- AlphaRING is a package designed for interpretable, protein structure-based prediction of missense variant deleteriousness.☆22Aug 6, 2025Updated 6 months ago
- QuickProt: A Fast and Accurate Homology-Based Protein Annotation Tool for Non-Model Organisms to Advance Comparative Genomics☆16Jan 12, 2026Updated last month
- Quickly generate consensus assemblies for bacterial genomes☆14Sep 12, 2025Updated 5 months ago
- Cython API for the Mutation Annotated Tree (MAT) Online Phylogenetics Toolkit☆14May 28, 2025Updated 9 months ago
- Inference of putative transmission phylogenetic clusters☆12Oct 13, 2020Updated 5 years ago
- Location of structural errors in a genome assembly and structural variations between a pair of genomes☆11Sep 27, 2019Updated 6 years ago
- Integrating influenza antigenic dynamics with molecular evolution☆12May 28, 2015Updated 10 years ago
- Taxonomy classification of viral sequences / contigs☆12Jul 15, 2025Updated 7 months ago
- A collection of documented examples using TreeTime☆22Jul 30, 2019Updated 6 years ago
- Influenza genome analysis Nextflow workflow☆31Sep 15, 2025Updated 5 months ago
- An R package for Standardized Summary, Annotation, Comparison, and Visualization of CNV, CNVR and ROH☆15Oct 17, 2021Updated 4 years ago
- A pipeline for bioinformatics analysis of bacterial genomes☆32Updated this week
- Script for removing or counting invariant sites for the RAxML ascertainment bias corrections☆16Oct 12, 2024Updated last year
- R Package for performing Qst-Fst analyses☆21Nov 14, 2017Updated 8 years ago
- Uses cDBG to count unitigs in bacterial populations☆16Feb 15, 2023Updated 3 years ago
- 🧬 Viral genome reference alignment☆12Jan 26, 2021Updated 5 years ago