tseemann / snp-distsView external linksLinks
Pairwise SNP distance matrix from a FASTA sequence alignment
☆151Dec 31, 2025Updated last month
Alternatives and similar repositories for snp-dists
Users that are interested in snp-dists are comparing it to the libraries listed below
Sorting:
- Create a tree using Mash distances☆182Oct 24, 2023Updated 2 years ago
- Rapid haploid variant calling and core genome alignment☆564Dec 12, 2025Updated 2 months ago
- Pan-genome wide association studies☆207May 29, 2024Updated last year
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins☆211Aug 27, 2025Updated 5 months ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Feb 15, 2019Updated 6 years ago
- Finds SNP sites from a multi-FASTA alignment file☆273Dec 16, 2020Updated 5 years ago
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆120May 21, 2024Updated last year
- "Reads to report" for public health and clinical microbiology☆143Dec 9, 2025Updated 2 months ago
- ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads☆252Dec 13, 2025Updated 2 months ago
- A set of scripts for calculating pairwise SNP distance☆44Jan 22, 2023Updated 3 years ago
- Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment☆16Dec 5, 2018Updated 7 years ago
- Assembly based core genome SNP alignments for bacteria☆25Oct 23, 2019Updated 6 years ago
- Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can b…☆149Oct 2, 2025Updated 4 months ago
- Scan contig files against PubMLST typing schemes☆263Jan 2, 2026Updated last month
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆94Dec 9, 2025Updated 2 months ago
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆103Updated this week
- A toolbox for pangenome analysis and threshold evaluation.☆99Jul 8, 2022Updated 3 years ago
- A tool for removing redundant genomes from a set of assemblies☆78Sep 10, 2025Updated 5 months ago
- a short-read polishing tool for long-read assemblies☆206Sep 19, 2025Updated 4 months ago
- Mass screening of contigs for antimicrobial and virulence genes☆475Jan 31, 2026Updated 2 weeks ago
- Antimicrobial Resistance Identification By Assembly☆184Oct 12, 2023Updated 2 years ago
- SEER, reimplemented in python 🐍🔮☆130May 22, 2025Updated 8 months ago
- Genome size estimation from long read overlaps☆80Dec 1, 2025Updated 2 months ago
- Split k-mer analysis – version 2☆104Jan 29, 2026Updated 2 weeks ago
- BSR-Based Allele Calling Algorithm☆148Feb 2, 2026Updated last week
- Recombination-free trees☆63Sep 1, 2025Updated 5 months ago
- AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and p…☆350Jan 31, 2026Updated 2 weeks ago
- Read alignment statistics for metagenomics☆387Jan 16, 2026Updated 3 weeks ago
- Bifrost graph gene caller.☆98Jan 20, 2026Updated 3 weeks ago
- An updated pipeline for pangenome investigation☆341Jan 15, 2026Updated 3 weeks ago
- Identify phage regions in bacterial genomes for masking purposes☆33Sep 5, 2019Updated 6 years ago
- Finding regions of similarity between plasmids☆17Nov 2, 2022Updated 3 years ago
- Rapid determination of appropriate reference genomes.☆99Jan 22, 2025Updated last year
- Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.☆235Oct 12, 2025Updated 4 months ago
- SKESA assembler☆124Oct 11, 2024Updated last year
- ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.☆290Feb 3, 2026Updated last week
- Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.☆186Feb 6, 2026Updated last week
- A flexible pipeline for complete analysis of bacterial genomes☆496Dec 19, 2025Updated last month
- a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome☆50Sep 23, 2022Updated 3 years ago