kwongj / maskrc-svgView external linksLinks
Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG
☆21Feb 15, 2019Updated 7 years ago
Alternatives and similar repositories for maskrc-svg
Users that are interested in maskrc-svg are comparing it to the libraries listed below
Sorting:
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆120May 21, 2024Updated last year
- RCandy: an R package for visualising homologous recombination events in bacterial genomes☆25Jun 17, 2022Updated 3 years ago
- Pairwise SNP distance matrix from a FASTA sequence alignment☆153Dec 31, 2025Updated last month
- Masks recombinant regions in an alignment based on ClonalFrameML output☆10May 18, 2018Updated 7 years ago
- Location of structural errors in a genome assembly and structural variations between a pair of genomes☆11Sep 27, 2019Updated 6 years ago
- Whole genome core alignments from multiple draft genomes☆13Sep 14, 2016Updated 9 years ago
- IS mapping software☆57Dec 3, 2021Updated 4 years ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆103Feb 9, 2026Updated last week
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆94Dec 9, 2025Updated 2 months ago
- Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment☆16Dec 5, 2018Updated 7 years ago
- ☆14Jun 30, 2021Updated 4 years ago
- post processing of bacterial pangenome gene presence/absence matrices☆63Jan 19, 2026Updated 3 weeks ago
- A bacterial GWAS pipeline written in Nextflow that uses Pyseer; Part III Project for Systems Biology at the University of Cambridge☆21Jan 20, 2026Updated 3 weeks ago
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins☆211Aug 27, 2025Updated 5 months ago
- Pan-genome wide association studies☆207May 29, 2024Updated last year
- My R scripts, primarily R plotting scripts + some genomics software including 16S rRNA metataxnomics and RNAseq☆12Dec 19, 2022Updated 3 years ago
- Trans-Kingdom Marker Gene Pipeline for Taxonomic Profiling of Human Metagenomes☆23Nov 24, 2025Updated 2 months ago
- Database and pipeline for protein structure-guided annotations of ecologically relevant functions at the metagenome scale.☆24Nov 2, 2025Updated 3 months ago
- Within-species genome-wide dN/dS estimation from very many genomes☆23Oct 26, 2020Updated 5 years ago
- Scripts to analyze gene content and make a concatenated alignment of core genes from bacterial genomes.☆19Jul 20, 2018Updated 7 years ago
- Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction☆249Updated this week
- ☆22Apr 20, 2023Updated 2 years ago
- Recombination-free trees☆63Sep 1, 2025Updated 5 months ago
- pGWAS and functional filtering pipeline to identify candidate adaptive genetic traits in bacteria☆11Feb 6, 2018Updated 8 years ago
- Tumor type classifier using cancer genomic panel sequencing data☆12Mar 12, 2024Updated last year
- Python module to manipulate and visualize minimap2's cs tag☆11Jul 28, 2024Updated last year
- rapid serotyping of Vibrio parahaemolyticus from whole genome sequencing data using serogroup-specific genes☆10Sep 2, 2021Updated 4 years ago
- Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.☆13Dec 24, 2025Updated last month
- A set of scripts for calculating pairwise SNP distance☆44Jan 22, 2023Updated 3 years ago
- Split Kmer Analysis☆66May 26, 2022Updated 3 years ago
- Application and Python module for average nucleotide identity analyses of microbes.☆217Jul 1, 2025Updated 7 months ago
- Phylogeny Enhanded Prediction of PAN-genome☆43Jul 17, 2020Updated 5 years ago
- Rapid haploid variant calling and core genome alignment☆565Dec 12, 2025Updated 2 months ago
- NCBI Pathogen Detection Portal toolkit☆11Sep 6, 2023Updated 2 years ago
- Program for finding horizontal gene transfer using BLAST result☆11May 26, 2023Updated 2 years ago
- Bacterial GWAS analysis☆46Jan 18, 2026Updated 3 weeks ago
- Visualization of the pan-genome output by panX☆66Jun 16, 2025Updated 8 months ago
- Streaming assembly for MinION data☆25Dec 16, 2023Updated 2 years ago
- Identify short variants and structural variants from raw sequencing data or genomic sequences☆34Mar 27, 2024Updated last year