ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
☆123Jun 2, 2026Updated last week
Alternatives and similar repositories for ClonalFrameML
Users that are interested in ClonalFrameML are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins☆220Aug 27, 2025Updated 9 months ago
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆98Dec 9, 2025Updated 6 months ago
- Pan-genome wide association studies☆219May 29, 2024Updated 2 years ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Feb 15, 2019Updated 7 years ago
- Whole genome core alignments from multiple draft genomes☆13Sep 14, 2016Updated 9 years ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Pairwise SNP distance matrix from a FASTA sequence alignment☆155Dec 31, 2025Updated 5 months ago
- treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes☆107Feb 6, 2025Updated last year
- A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome☆109Dec 5, 2025Updated 6 months ago
- Locus and lineage tests for bacterial GWAS☆28Oct 5, 2017Updated 8 years ago
- Reconstruction of transmission trees using genomic data☆72Sep 27, 2023Updated 2 years ago
- Pipeline for analysing intergenic regions in bacteria☆39Oct 25, 2019Updated 6 years ago
- an interactive viewer for populations of bacterial genomes linked by a phylogeny☆133Feb 26, 2024Updated 2 years ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆108Jun 2, 2026Updated last week
- Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.☆122May 29, 2026Updated last week
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Interactive, web tool for exploring pan-genome of bacterial strains☆50Jan 14, 2026Updated 4 months ago
- Bacterial phylogenetics in BEAST 2.☆18Mar 30, 2023Updated 3 years ago
- Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can b…☆155Oct 2, 2025Updated 8 months ago
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆50May 18, 2026Updated 3 weeks ago
- Rapid large-scale prokaryote pan genome analysis☆379Nov 3, 2025Updated 7 months ago
- "Reads to report" for public health and clinical microbiology☆144Dec 9, 2025Updated 6 months ago
- Rapid determination of appropriate reference genomes.☆101Jan 22, 2025Updated last year
- Scan contig files against PubMLST typing schemes☆285Mar 26, 2026Updated 2 months ago
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆646May 15, 2026Updated 3 weeks ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Fast Whole-Genome Similarity (ANI) Estimation☆463Dec 16, 2025Updated 5 months ago
- Split Kmer Analysis☆66May 26, 2022Updated 4 years ago
- (a) (p)erfect (c)ircle? ... tests DNA sequences for overlapping ends, then trims and rejoins, and aligns reads to test the join☆10Apr 29, 2021Updated 5 years ago
- Application and Python module for average nucleotide identity analyses of microbes.☆217Jul 1, 2025Updated 11 months ago
- A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.☆127Oct 30, 2023Updated 2 years ago
- Masks recombinant regions in an alignment based on ClonalFrameML output☆10May 18, 2018Updated 8 years ago
- An updated pipeline for pangenome investigation☆361Jun 2, 2026Updated last week
- Rapid haploid variant calling and core genome alignment☆586Dec 12, 2025Updated 5 months ago
- Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.☆253May 13, 2026Updated 3 weeks 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.
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆27Aug 8, 2022Updated 3 years ago
- SEER, reimplemented in python 🐍🔮☆135Mar 24, 2026Updated 2 months ago
- Create a tree using Mash distances☆188Oct 24, 2023Updated 2 years ago
- Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction☆252Jun 1, 2026Updated last week
- Split k-mer analysis – version 2☆104Apr 9, 2026Updated 2 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Jun 26, 2018Updated 7 years ago
- Inferring bacterial recombination rates from large-scale sequencing datasets.☆41Feb 25, 2023Updated 3 years ago