Code for the paper "Learning the fitness dynamics of pathogens from phylogenies"
☆26Feb 26, 2026Updated 6 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. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Repository containing a method for automatically identifying pathogen lineages from a phylogeny.☆17May 19, 2023Updated 3 years ago
- Prediction fitness of leaves on a genealogical tree☆12May 7, 2015Updated 11 years ago
- Analysing the genomic context of mobile genes☆11Jul 21, 2025Updated last year
- Inferring spatiotemporal dynamics of H5N1 influenza from sequence data☆10Sep 6, 2013Updated 13 years ago
- Inferring global and local strict molecular clocks using root-to-tip regression☆20Jun 30, 2026Updated 2 months ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- ☆20Nov 11, 2024Updated last year
- Fast pairwise transmission inference from single genome and/or metagenomic data☆37Aug 21, 2026Updated 2 weeks ago
- kMetaShot is an alignment-free taxonomic classifier based on k-mer/minimizer counting for MAGs☆12Apr 27, 2026Updated 4 months ago
- A toolkit for quality control & adjustment of nucleotide redundancy in bacterial pan-genome analyses☆21Feb 12, 2026Updated 6 months ago
- Order and orientation of complete bacterial genomes☆29Jun 30, 2026Updated 2 months ago
- Fast, scalable, accurate and accessible Bayesian phylogenetics☆46Aug 27, 2026Updated last week
- A DRAFT, early stage book on snakemake.☆24Nov 1, 2023Updated 2 years ago
- Retrieve HIVdb algorithm as XML and apply locally to HIV sequences☆14Aug 13, 2026Updated 3 weeks ago
- Racmacs R package for performing antigenic cartography☆24Jul 8, 2026Updated 2 months ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- MAPLE - a new approximate approach for maximum likelihood phylogenetics at short divergence.☆66Mar 15, 2026Updated 5 months ago
- An open-source pathogen sequence database dedicated to equitable sharing, transparent governance, & empowering global public health.☆59Aug 31, 2026Updated last week
- Simple Manipulation Of Trees☆14Aug 16, 2025Updated last year
- Iterative Gene clUster Analysis, a high-throughput method for gene cluster family identification.☆20Aug 19, 2026Updated 2 weeks ago
- Stitch together Nanopore tiled amplicon data without polishing a reference☆18Jan 29, 2024Updated 2 years ago
- This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.☆21Mar 18, 2026Updated 5 months ago
- Visualize microbial evolution at the SNP level!☆16Aug 12, 2025Updated last year
- ☆11Dec 20, 2022Updated 3 years ago
- Fast and accurate tool for calculating Average Nucleotide Identity (ANI) and clustering virus genomes and metagenomes☆111Jul 7, 2026Updated 2 months ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- BItsliced Genomic Signature Index - Efficient indexing and search in very large collections of WGS data☆10Jun 13, 2023Updated 3 years ago
- app to collapse Pango lineages for reporting☆13Dec 9, 2025Updated 8 months ago
- FASTQ-to-CodFreq pipeline for HIV-1 and SARS-CoV-2☆15Aug 12, 2025Updated last year
- ISCompare, an opensource program to identify Differentially Located Insertion Sequences☆14Apr 30, 2026Updated 4 months ago
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆25Jun 17, 2022Updated 4 years ago
- Simple-to-use interactive comparison of two bacterial genomes☆28Jan 30, 2026Updated 7 months ago
- VILOCA: VIral LOcal haplotype reconstruction and mutation CAlling for short and long read data☆23Oct 21, 2025Updated 10 months ago
- Population analysis PIPEline 🛠🧬☆26Mar 2, 2026Updated 6 months ago
- Resolving Species Level Classification Using Emu☆14Jun 14, 2024Updated 2 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Plasmid analysis using rearrangement distances☆56Jul 19, 2026Updated last month
- This repository contains python classes and functions to quickly create a profiling tool for pathogen NGS data☆14Aug 25, 2026Updated last week
- Global phylogenies of SARS-CoV-2 sequences☆86Oct 24, 2023Updated 2 years ago
- Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.☆55Mar 23, 2026Updated 5 months ago
- Dryad is a Nextflow pipeline for examining prokaryote relatedness. Dryad can perform a reference free analysis and/or SNP analysis.☆21Aug 17, 2026Updated 3 weeks ago
- A Swiss-Army-Knife for Bioinformaticians☆15Jul 26, 2026Updated last month
- Mutual nearest neighbor graphs for population structure inference and visualization☆18Dec 4, 2025Updated 9 months ago