noemielefrancq / Phylowave_Learning-fitness-dynamics-pathogens-in-phylogenies
Code for the paper "Learning the fitness dynamics of pathogens from phylogenies"
☆17Updated 3 weeks 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:
- Inferring global and local strict molecular clocks using root-to-tip regression☆13Updated 9 months ago
- A tool to identify and annotate homoplasies on a phylogeny and sequence alignment☆20Updated 3 years ago
- 🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables☆27Updated last year
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆48Updated 2 years ago
- Fast, scalable, accurate and accessible Bayesian phylogenetics☆37Updated last week
- Bacterial phylogenetics in BEAST 2.☆17Updated 2 years ago
- SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.☆13Updated 3 years ago
- A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data☆62Updated 2 years ago
- ☆17Updated 11 months ago
- Phylogenetic maximum representation sampling: choosing most representative strains or taxa☆38Updated last month
- Interpretative standards for AMR genotypes☆18Updated this week
- R package for microbial pangenomics☆23Updated 3 years ago
- Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs☆24Updated 9 months ago
- Recombination-free trees☆58Updated last month
- Metagenomic Analysis in Real Time☆24Updated last month
- Reconstruction of transmission trees using genomic data☆62Updated last year
- BEAV: Bacterial Element Annotation reVamped☆65Updated 6 months ago
- Discover and annotate the virome☆42Updated last month
- CroCoDeEL is a tool that detects cross-sample contamination in shotgun metagenomic data☆24Updated this week
- ☆17Updated this week
- Working with the outputs of sourmash in R☆27Updated last year
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆27Updated 6 months ago
- Calculate assocations between genes and traits☆23Updated 2 months ago
- Small utility script to submit genomes to PHASTER for phage detection☆24Updated 3 years ago
- Fast pairwise transmission inference from single genome and/or metagenomic data☆21Updated 7 months ago
- spruceup☆24Updated 8 months ago
- Two-dimensional outlier detection algorithm for pinpointing errors in small species-specific stretches of the multiple sequence alignment…☆13Updated 11 months ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆45Updated 3 weeks ago
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆26Updated 5 years ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆28Updated last year