ChrispinChaguza / RCandy
RCandy: an R package for visualising homologous recombination events in bacterial genomes
☆19Updated 2 years ago
Alternatives and similar repositories for RCandy:
Users that are interested in RCandy are comparing it to the libraries listed below
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆56Updated 2 weeks ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆20Updated 6 years ago
- Inferring bacterial recombination rates from large-scale sequencing datasets.☆42Updated 2 years ago
- An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences☆25Updated 2 years ago
- Plasmid analysis using rearrangement distances☆33Updated 4 months ago
- Gene-flank analysis tool☆27Updated 3 months ago
- Genomewide Epistasis Analysis on Bacteria☆14Updated 6 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆50Updated 8 months ago
- skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes.☆44Updated last week
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆26Updated 4 months ago
- Calculate assocations between genes and traits☆23Updated last week
- Extracts contigs harbouring a target gene / sequence from assemblies and aligns the contigs around the target sequence☆13Updated 6 years ago
- Fast pairwise transmission inference from single genome and/or metagenomic data☆19Updated 5 months ago
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆26Updated last month
- A k-mer based program for the identification of known plasmids from whole-genome sequencing reads☆35Updated 4 years ago
- Discover and annotate the virome☆39Updated 5 months ago
- Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes☆34Updated last month
- IslandPath standalone software☆31Updated last year
- Automated strain separation of low-complexity metagenomes☆51Updated 3 years ago
- Bacterial GWAS analysis☆37Updated last week
- pGWAS and functional filtering pipeline to identify candidate adaptive genetic traits in bacteria☆11Updated 7 years ago
- A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes☆18Updated last year
- Recombination-free trees☆57Updated last year
- SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.☆13Updated 2 years ago
- Miscellaneous Perl scripts from 20 years in microbial bioinformatics☆17Updated 8 months ago
- A Python implementation of the OrthoANI algorithm for nucleotide identity measurement.☆24Updated last week
- Genome size estimation from long read overlaps☆50Updated 3 months ago
- Microbial agile accurate SNP Typer☆29Updated last year
- Calculate Average Nucleotide Identity (ANI) for prokaryotic genomes☆19Updated 2 years ago