Masks recombinant regions in an alignment based on ClonalFrameML output
☆10May 18, 2018Updated 8 years ago
Alternatives and similar repositories for cfml-maskrc
Users that are interested in cfml-maskrc are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Feb 15, 2019Updated 7 years ago
- Tool for visualising viral lineages in space and time. As seen on covid19.sanger.ac.uk and covglobe.org.☆10Jul 22, 2022Updated 4 years ago
- Bacterial Operon Finder for Functional Organization☆16Nov 14, 2023Updated 2 years ago
- assorted scripts for doing genomics☆13Nov 23, 2015Updated 10 years ago
- Whole genome core alignments from multiple draft genomes☆13Sep 14, 2016Updated 10 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.
- Formats Roary output for viewing in FriPan☆11May 23, 2018Updated 8 years ago
- Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment☆16Dec 5, 2018Updated 7 years ago
- A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concat…☆60May 7, 2026Updated 6 months ago
- A comprehensive toolkit for running Oxford Nanopore's MinION☆12Oct 11, 2018Updated 8 years ago
- Archived - please see updated sccmec tool at link below☆13Aug 30, 2024Updated 2 years ago
- ☆18Mar 11, 2024Updated 2 years ago
- variant discovery and annotation using GATK and Ensembl☆17Jun 27, 2013Updated 13 years ago
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆131Jun 2, 2026Updated 5 months ago
- REcombination BARcode detector.☆17Apr 2, 2024Updated 2 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- pipeline for read mapping, snp calling and annotation for bacterial genomes☆13Mar 12, 2024Updated 2 years ago
- Pairwise SNP distance matrix from a FASTA sequence alignment☆158Dec 31, 2025Updated 10 months ago
- Global phylogenies of SARS-CoV-2 sequences☆87Oct 24, 2023Updated 3 years ago
- Locus and lineage tests for bacterial GWAS☆28Oct 5, 2017Updated 9 years ago
- ☆16Oct 2, 2019Updated 7 years ago
- Clermont PCR method In-Silico☆28Feb 8, 2024Updated 2 years ago
- Generate mutated sequence files from a reference genome.☆11Oct 14, 2026Updated 3 weeks ago
- Pan-genome wide association studies☆229May 29, 2024Updated 2 years ago
- ASMNGS20 - 2020 Conference Details☆15Jun 10, 2022Updated 4 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.
- Large scale Blast Score Ratio (BSR) analysis☆36Nov 18, 2025Updated 11 months ago
- a re-packaging of the sankey plot function for kraken reports taken from pavian and sankeyD3 from Florian Breitwieser☆15Dec 5, 2025Updated 11 months ago
- Genome comparison via de Bruijn graph. To get the latest stable version, please visit our site.☆70Oct 29, 2020Updated 6 years ago
- A draft genome scaffolder that uses multiple reference genomes in a graph-based approach.☆47Feb 17, 2021Updated 5 years ago
- A pipeline to investigate horizontal gene transfer from NGS data☆27Updated this week
- ☆16Jun 21, 2023Updated 3 years ago
- Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input…☆36May 1, 2022Updated 4 years ago
- A simple program to classify the lifestyle of phages.☆18May 22, 2023Updated 3 years ago
- Interactive, web tool for exploring pan-genome of bacterial strains☆50Jan 14, 2026Updated 9 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.
- (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
- Rapidly subtype microbial genomes using single-nucleotide variant (SNV) subtyping schemes☆28Dec 9, 2024Updated last year
- DDBJ Fast Annotation and Submission Tool☆86Updated this week
- Phylogeny Enhanded Prediction of PAN-genome☆45Jul 17, 2020Updated 6 years ago
- Munge GenBank files into FASTA and tab-separated metadata☆15Feb 5, 2026Updated 9 months ago
- app to collapse Pango lineages for reporting☆14Oct 2, 2026Updated last month
- Inference of homologous recombination in bacteria using whole genome sequences☆10Sep 26, 2025Updated last year