ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
☆120May 21, 2024Updated last year
Alternatives and similar repositories for ClonalFrameML
Users that are interested in ClonalFrameML are comparing it to the libraries listed below
Sorting:
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins☆213Aug 27, 2025Updated 6 months ago
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆95Dec 9, 2025Updated 2 months ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Feb 15, 2019Updated 7 years ago
- Pan-genome wide association studies☆208May 29, 2024Updated last year
- Pairwise SNP distance matrix from a FASTA sequence alignment☆153Dec 31, 2025Updated 2 months ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆104Feb 9, 2026Updated 2 weeks ago
- treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes☆106Feb 6, 2025Updated last year
- 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
- Whole genome core alignments from multiple draft genomes☆13Sep 14, 2016Updated 9 years ago
- A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome☆104Dec 5, 2025Updated 2 months ago
- Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.☆122Jan 22, 2025Updated last year
- Split Kmer Analysis☆66May 26, 2022Updated 3 years ago
- an interactive viewer for populations of bacterial genomes linked by a phylogeny☆131Feb 26, 2024Updated 2 years ago
- Locus and lineage tests for bacterial GWAS☆28Oct 5, 2017Updated 8 years ago
- Rapid large-scale prokaryote pan genome analysis☆371Nov 3, 2025Updated 3 months ago
- Bacterial phylogenetics in BEAST 2.☆18Mar 30, 2023Updated 2 years ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆49Jan 14, 2026Updated last month
- 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…☆152Oct 2, 2025Updated 4 months ago
- Split k-mer analysis – version 2☆104Jan 29, 2026Updated last month
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆607Feb 18, 2026Updated last week
- Scan contig files against PubMLST typing schemes☆267Jan 2, 2026Updated last month
- Create a tree using Mash distances☆182Oct 24, 2023Updated 2 years ago
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆50Apr 16, 2024Updated last year
- SEER, reimplemented in python 🐍🔮☆131May 22, 2025Updated 9 months ago
- An updated pipeline for pangenome investigation☆344Jan 15, 2026Updated last month
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆27Aug 8, 2022Updated 3 years ago
- Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction☆249Updated this week
- Recombination-free trees☆63Sep 1, 2025Updated 6 months ago
- Rapid determination of appropriate reference genomes.☆100Jan 22, 2025Updated last year
- Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.☆235Oct 12, 2025Updated 4 months ago
- Fast Whole-Genome Similarity (ANI) Estimation☆447Dec 16, 2025Updated 2 months ago
- Application and Python module for average nucleotide identity analyses of microbes.☆217Jul 1, 2025Updated 8 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Jun 26, 2018Updated 7 years ago
- MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies☆168Apr 16, 2025Updated 10 months ago
- Reorients assembled microbial sequences☆133Aug 21, 2025Updated 6 months ago
- a short-read polishing tool for long-read assemblies☆207Sep 19, 2025Updated 5 months ago
- a collection of scripts for organising bacterial genomes by species☆81Mar 18, 2022Updated 3 years ago
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆36Feb 3, 2021Updated 5 years ago