Inference of homologous recombination in bacteria using whole genome sequences
☆10Sep 26, 2025Updated last year
Alternatives and similar repositories for ClonalOrigin
Users that are interested in ClonalOrigin are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- MUMmer3☆17Jan 12, 2022Updated 4 years ago
- A selection of short scripts for analyzing microbial genomes☆14Jun 26, 2018Updated 8 years ago
- Bacterial phylogenetics in BEAST 2.☆20Sep 17, 2026Updated last month
- plot Multiple Sequence Alignment(MSA) of Clustal by python package☆15Mar 14, 2023Updated 3 years ago
- Formats Roary output for viewing in FriPan☆11May 23, 2018Updated 8 years ago
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Feb 15, 2019Updated 7 years ago
- Experiments with using BIGSI data structure for metagenomic and QC applications☆19Aug 12, 2024Updated 2 years ago
- Phasing of dikaryotic fungal genome assemblies☆13Mar 1, 2023Updated 3 years ago
- Detecting recombination of viral lineages☆11Dec 23, 2025Updated 10 months ago
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆130Jun 2, 2026Updated 4 months ago
- waka waka☆18Mar 18, 2021Updated 5 years ago
- Finding prophage regions in bacterial genomes using brute force☆22Jan 20, 2023Updated 3 years ago
- Pangenome analysis of eukaryotes.☆21Sep 21, 2020Updated 6 years ago
- abi2fastq is a small utility to convert Sanger sequencing reads in .abi (applied biosystems) format to FASTQ☆13Sep 19, 2017Updated 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.
- Rapid discovery of reciprocal best blast pairs.☆10Nov 9, 2024Updated last year
- Sequence simulator☆55Feb 3, 2025Updated last year
- plotnineSeqSuite: a Python package for visualizing sequence data using ggplot2 style☆18Dec 19, 2025Updated 10 months ago
- ☆23Dec 9, 2025Updated 10 months ago
- Hamiltonian Monte Carlo on the space of phylogenies☆10Apr 20, 2017Updated 9 years ago
- NCBI Pathogen Detection Portal toolkit☆11Sep 6, 2023Updated 3 years ago
- Predict MLST directly from uncorrected long reads☆27Oct 31, 2025Updated 11 months 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…☆159Sep 2, 2026Updated last month
- assorted scripts for doing genomics☆13Nov 23, 2015Updated 10 years 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.
- Prediction of apoplastic and cytoplasmic effectors in fungi and oomycetes☆27Mar 31, 2026Updated 6 months ago
- Tutorial about R package PopGenome☆44Mar 1, 2019Updated 7 years ago
- (a) (p)erfect (c)ircle? ... tests DNA sequences for overlapping ends, then trims and rejoins, and aligns reads to test the join☆11Apr 29, 2021Updated 5 years ago
- A set of scripts to help automate the construction of data sets for multi-gene phylogenetic analyses.☆13Mar 13, 2019Updated 7 years ago
- Renames headers in FASTA file☆13Jun 28, 2017Updated 9 years ago
- ☆15Apr 19, 2018Updated 8 years ago
- orthology assignment using phylogenetic and network analyses☆58Oct 1, 2026Updated 3 weeks ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆31Jul 18, 2025Updated last year
- AUGUSTUS v3.2.1 for installation on Mac OS X☆12May 21, 2018Updated 8 years 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.
- Introduction to Nanopore Sequencing - Prac material and presentations from The Omics Australia Tutorials Sydney (TOAST) workshop 19th - 2…☆10Jan 12, 2019Updated 7 years ago
- An RNA virus strain-level identification tool for short reads.☆23Apr 6, 2026Updated 6 months ago
- Perl and Python scripts allowing to get sequence information from GenBank, RefSeq or ENA sequence repositories☆14Mar 29, 2025Updated last year
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆16Jun 26, 2018Updated 8 years ago
- ☆11Apr 11, 2017Updated 9 years ago
- LYVE-SET, a method of using hqSNPs to create a phylogeny, especially for outbreak investigations☆26Aug 26, 2024Updated 2 years ago
- R We There Yet?☆33Mar 27, 2025Updated last year