noemielefrancq / Phylowave_Learning-fitness-dynamics-pathogens-in-phylogeniesView external linksLinks
Code for the paper "Learning the fitness dynamics of pathogens from phylogenies"
☆23Nov 24, 2025Updated 2 months ago
Alternatives and similar repositories for Phylowave_Learning-fitness-dynamics-pathogens-in-phylogenies
Users that are interested in Phylowave_Learning-fitness-dynamics-pathogens-in-phylogenies are comparing it to the libraries listed below
Sorting:
- Analysing the genomic context of mobile genes☆11Jul 21, 2025Updated 6 months ago
- Inferring global and local strict molecular clocks using root-to-tip regression☆15Nov 17, 2025Updated 3 months ago
- ☆19Nov 11, 2024Updated last year
- Order and orientation of complete bacterial genomes☆29Jul 11, 2025Updated 7 months ago
- Population analysis PIPEline 🛠🧬☆22Feb 3, 2026Updated 2 weeks ago
- A toolkit for quality control & adjustment of nucleotide redundancy in bacterial pan-genome analyses☆21Updated this week
- This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.☆21May 16, 2023Updated 2 years ago
- Fast pairwise transmission inference from single genome and/or metagenomic data☆23Aug 1, 2025Updated 6 months ago
- Inferring spatiotemporal dynamics of H5N1 influenza from sequence data☆10Sep 6, 2013Updated 12 years ago
- ☆11Updated this week
- BItsliced Genomic Signature Index - Efficient indexing and search in very large collections of WGS data☆10Jun 13, 2023Updated 2 years ago
- Iterative Gene clUster Analysis, a high-throughput method for gene cluster family identification.☆17Feb 9, 2026Updated last week
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆25Jun 17, 2022Updated 3 years ago
- Prediction fitness of leaves on a genealogical tree☆12May 7, 2015Updated 10 years ago
- ISCompare, an opensource program to identify Differentially Located Insertion Sequences☆14Jul 30, 2024Updated last year
- mGEMS Genomic epidemiology with mixed samples☆15Sep 4, 2024Updated last year
- Visualize microbial evolution at the SNP level!☆15Aug 12, 2025Updated 6 months ago
- PowerBacGWAS: Power calculations for Bacterial GWAS☆13Feb 2, 2022Updated 4 years ago
- This repository contains python classes and functions to quickly create a profiling tool for pathogen NGS data☆12Dec 1, 2025Updated 2 months ago
- SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.☆15Apr 29, 2022Updated 3 years ago
- Mutual nearest neighbor graphs for population structure inference and visualization☆18Dec 4, 2025Updated 2 months ago
- mSWEEP High-resolution sweep metagenomics using fast probabilistic inference☆15Nov 19, 2025Updated 2 months ago
- Simulate mutations in genomes☆15Jun 15, 2020Updated 5 years ago
- Organism-specific interpretation of AMR genotypes☆15Mar 13, 2024Updated last year
- A toolbox for pangenome analysis and threshold evaluation.☆99Jul 8, 2022Updated 3 years ago
- ☆18Jun 11, 2024Updated last year
- ☆26Updated this week
- A library of Machine Learning tools to predict antibiotic resistance from NGS data☆18May 30, 2022Updated 3 years ago
- Dryad is a Nextflow pipeline for examining prokaryote relatedness. Dryad can perform a reference free analysis and/or SNP analysis.☆18Nov 20, 2025Updated 2 months ago
- transposable element typing pipeline☆19Mar 8, 2024Updated last year
- Racmacs R package for performing antigenic cartography☆24Jun 27, 2024Updated last year
- Quantifying the significance of genetic variation using probabilistic profile-based methods.☆19Apr 21, 2021Updated 4 years ago
- Color DNA/RNA bases in terminal output☆21Aug 29, 2017Updated 8 years ago
- Support scripts for the visualisation of pangenome analyses in Graphia☆21Oct 7, 2024Updated last year
- Simple-to-use interactive comparison of two bacterial genomes☆25Jan 30, 2026Updated 2 weeks ago
- Plasmid analysis using rearrangement distances☆50Jan 23, 2026Updated 3 weeks ago
- Bacterial phylogenetics in BEAST 2.☆18Mar 30, 2023Updated 2 years ago
- Targeted Detection and Reconstruction of Plasmids☆22May 7, 2024Updated last year
- ☆22Apr 20, 2023Updated 2 years ago