RCandy: an R package for visualising homologous recombination events in bacterial genomes
☆25Jun 17, 2022Updated 3 years ago
Alternatives and similar repositories for RCandy
Users that are interested in RCandy are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Analysing the genomic context of mobile genes☆11Jul 21, 2025Updated 9 months ago
- A toolkit for quality control & adjustment of nucleotide redundancy in bacterial pan-genome analyses☆21Feb 12, 2026Updated 2 months ago
- Extracts contigs harbouring a target gene / sequence from assemblies and aligns the contigs around the target sequence☆13May 15, 2018Updated 7 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆65Jun 16, 2025Updated 10 months ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Feb 15, 2019Updated 7 years ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- post processing of bacterial pangenome gene presence/absence matrices☆66Jan 19, 2026Updated 3 months ago
- Iterative Gene clUster Analysis, a high-throughput method for gene cluster family identification.☆17Feb 26, 2026Updated 2 months ago
- Population analysis PIPEline 🛠🧬☆24Mar 2, 2026Updated 2 months ago
- Fast pairwise transmission inference from single genome and/or metagenomic data☆32Aug 1, 2025Updated 9 months ago
- All scripts used for the analysis of the twilight of the pan-genome, and scripts available for others to apply similar analysis☆19Mar 30, 2021Updated 5 years ago
- Location of structural errors in a genome assembly and structural variations between a pair of genomes☆11Sep 27, 2019Updated 6 years ago
- ☆13Mar 28, 2018Updated 8 years ago
- HMmer Based UndeRstandinG of gene clustERs☆15Feb 6, 2026Updated 3 months ago
- Rapid determination of appropriate reference genomes.☆101Jan 22, 2025Updated last year
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- ☆15Mar 14, 2023Updated 3 years ago
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.☆36Jul 21, 2025Updated 9 months ago
- Uses cDBG to count unitigs in bacterial populations☆16Feb 15, 2023Updated 3 years ago
- SEER, reimplemented in python 🐍🔮☆133Mar 24, 2026Updated last month
- This program is designed for annotation of antimicrobal resistance(AMR), transposon(Tn) and integron(In) in bacteria.☆21Mar 18, 2026Updated last month
- Bioinformatics tool for Locus Visualisation☆165Mar 30, 2026Updated last month
- Plasmid analysis using rearrangement distances☆53Apr 30, 2026Updated last week
- Inferring bacterial recombination rates from large-scale sequencing datasets.☆41Feb 25, 2023Updated 3 years ago
- Within-species genome-wide dN/dS estimation from very many genomes☆23Oct 26, 2020Updated 5 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- IS mapping software☆58Dec 3, 2021Updated 4 years ago
- A Whole Genome Alignment Visualization Tool for the Web☆44Apr 29, 2023Updated 3 years ago
- An R package designed for drawing gene arrow maps☆99Sep 29, 2025Updated 7 months ago
- Mandrake 🌿/👨🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding☆39Mar 7, 2025Updated last year
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆636Feb 18, 2026Updated 2 months ago
- R package for microbial pangenomics☆24Apr 12, 2022Updated 4 years ago
- Compute a pairwise SNP distance matrix from one or two alignment(s)☆26Sep 12, 2024Updated last year
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆108Mar 2, 2026Updated 2 months ago
- Gene cluster comparison figure generator☆641Dec 22, 2025Updated 4 months 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.
- Support scripts for the visualisation of pangenome analyses in Graphia☆21Oct 7, 2024Updated last year
- A minimap2 implementation with binseq inputs☆17Dec 11, 2025Updated 4 months ago
- Gene-flank analysis tool☆37Dec 18, 2024Updated last year
- Order and orientation of complete bacterial genomes☆29Jul 11, 2025Updated 9 months ago
- Homebrew formulae for bioinformatics software only available for Linux☆27Aug 23, 2019Updated 6 years ago
- A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category☆83May 3, 2025Updated last year
- Detection of pseudogene candidates in bacterial and archaeal genomes.☆52Mar 22, 2024Updated 2 years ago