ChrispinChaguza / RCandyView external linksLinks
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
Sorting:
- Analysing the genomic context of mobile genes☆11Jul 21, 2025Updated 6 months ago
- A toolkit for quality control & adjustment of nucleotide redundancy in bacterial pan-genome analyses☆21Updated this week
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Feb 15, 2019Updated 7 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆65Jun 16, 2025Updated 7 months ago
- post processing of bacterial pangenome gene presence/absence matrices☆63Jan 19, 2026Updated 3 weeks ago
- Iterative Gene clUster Analysis, a high-throughput method for gene cluster family identification.☆17Jan 31, 2026Updated 2 weeks 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 4 years ago
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.☆34Jul 21, 2025Updated 6 months ago
- Location of structural errors in a genome assembly and structural variations between a pair of genomes☆11Sep 27, 2019Updated 6 years ago
- Fast pairwise transmission inference from single genome and/or metagenomic data☆23Aug 1, 2025Updated 6 months ago
- A minimap2 implementation with binseq inputs☆17Dec 11, 2025Updated 2 months ago
- ☆15Mar 14, 2023Updated 2 years ago
- Uses cDBG to count unitigs in bacterial populations☆16Feb 15, 2023Updated 3 years ago
- ☆13Mar 28, 2018Updated 7 years ago
- Inferring bacterial recombination rates from large-scale sequencing datasets.☆41Feb 25, 2023Updated 2 years ago
- Bioinformatics tool for Locus Visualisation☆159Jan 24, 2026Updated 3 weeks ago
- R package for microbial pangenomics☆24Apr 12, 2022Updated 3 years ago
- Extracts contigs harbouring a target gene / sequence from assemblies and aligns the contigs around the target sequence☆13May 15, 2018Updated 7 years ago
- HMmer Based UndeRstandinG of gene clustERs☆15Feb 6, 2026Updated last week
- Fast sequence distance estimates☆26Jan 29, 2026Updated 2 weeks ago
- Plasmid analysis using rearrangement distances☆50Jan 23, 2026Updated 3 weeks ago
- A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category☆81May 3, 2025Updated 9 months ago
- Population analysis PIPEline 🛠🧬☆22Feb 3, 2026Updated last week
- SEER, reimplemented in python 🐍🔮☆130May 22, 2025Updated 8 months ago
- RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches☆53Feb 4, 2026Updated last week
- Simple-to-use interactive comparison of two bacterial genomes☆22Jan 30, 2026Updated 2 weeks ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆103Updated this week
- Gene-flank analysis tool☆37Dec 18, 2024Updated last year
- Rapid determination of appropriate reference genomes.☆99Jan 22, 2025Updated last year
- A toolbox for pangenome analysis and threshold evaluation.☆99Jul 8, 2022Updated 3 years ago
- Code for the paper "Learning the fitness dynamics of pathogens from phylogenies"☆23Nov 24, 2025Updated 2 months ago
- Support scripts for the visualisation of pangenome analyses in Graphia☆21Oct 7, 2024Updated last year
- ☆82Nov 27, 2025Updated 2 months ago
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆606Updated this week
- A tool for drawing ANI clustermap between all-vs-all microbial genomes☆91May 3, 2025Updated 9 months ago
- IS mapping software☆57Dec 3, 2021Updated 4 years ago
- An R package designed for drawing gene arrow maps☆95Sep 29, 2025Updated 4 months ago
- Gene cluster comparison figure generator☆635Dec 22, 2025Updated last month
- Within-species genome-wide dN/dS estimation from very many genomes☆23Oct 26, 2020Updated 5 years ago