noemielefrancq / Phylowave_Learning-fitness-dynamics-pathogens-in-phylogenies
Code for the paper "Learning the fitness dynamics of pathogens from phylogenies"
☆15Updated this week
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
- R package for microbial pangenomics☆23Updated 2 years ago
- Fast, scalable, accurate and accessible Bayesian phylogenetics☆33Updated this week
- Phylogenetic maximum representation sampling: choosing most representative strains or taxa☆37Updated 3 months ago
- A tool to identify and annotate homoplasies on a phylogeny and sequence alignment☆20Updated 3 years ago
- ☆17Updated 9 months ago
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆48Updated 2 years ago
- ☆17Updated 3 weeks ago
- Spatial Phylogenetic Reconstruction of Evolutionary Dynamics 3☆15Updated last year
- Bacterial phylogenetics in BEAST 2.☆17Updated last year
- Scalable relaxed clock phylogenetic dating☆24Updated 11 months ago
- ☆16Updated last week
- Inferring global and local strict molecular clocks using root-to-tip regression☆11Updated 8 months ago
- Influenza data pipeline to automate genotyping assignment☆29Updated last month
- 🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables☆27Updated last year
- Unleash the full power of your k-mers!☆14Updated last week
- Recombination-free trees☆57Updated last year
- A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data☆61Updated 2 years ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆36Updated 2 weeks ago
- Fast pairwise transmission inference from single genome and/or metagenomic data☆19Updated 5 months ago
- starfish: a modular toolkit for giant mobile element annotation☆29Updated 3 months ago
- Metagenomic Analysis in Real Time☆23Updated this week
- Virus reassortment inference software. Infers both recent and ancestral reassortment and uses flexible molecular clock constraints.☆12Updated last month
- SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.☆13Updated 2 years ago
- Interpretative standards for AMR genotypes☆18Updated 8 months ago
- ☆35Updated 3 weeks ago
- MutTui pipeline to reconstruct mutational spectra for bacterial and viral datasets☆28Updated 8 months ago
- BEAV: Bacterial Element Annotation reVamped☆62Updated 4 months ago
- An `R` package for various phylogenetic and evolutionary biology data manipulations☆12Updated 7 years ago
- A pipeline for performing genome-wide association tests for bacterial genomes.☆27Updated 6 years ago
- Predict plasmids from uncorrected long read data☆39Updated 5 years ago