Pairwise SNP distance matrix from a FASTA sequence alignment
☆156Dec 31, 2025Updated 8 months ago
Alternatives and similar repositories for snp-dists
Users that are interested in snp-dists are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Rapid haploid variant calling and core genome alignment☆591Dec 12, 2025Updated 8 months ago
- Pan-genome wide association studies☆223May 29, 2024Updated 2 years ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Feb 15, 2019Updated 7 years ago
- A set of scripts for calculating pairwise SNP distance☆45Feb 19, 2026Updated 6 months ago
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆127Jun 2, 2026Updated 3 months ago
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- Create a tree using Mash distances☆188Oct 24, 2023Updated 2 years ago
- Finds SNP sites from a multi-FASTA alignment file☆278Dec 16, 2020Updated 5 years ago
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins☆224Aug 27, 2025Updated last year
- Assembly based core genome SNP alignments for bacteria☆25Oct 23, 2019Updated 6 years ago
- "Reads to report" for public health and clinical microbiology☆144Dec 9, 2025Updated 8 months ago
- Scan contig files against PubMLST typing schemes☆298Jun 17, 2026Updated 2 months ago
- ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads☆264Jun 11, 2026Updated 2 months 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…☆157Updated this week
- Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment☆16Dec 5, 2018Updated 7 years ago
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆99Dec 9, 2025Updated 8 months ago
- BSR-Based Allele Calling Algorithm☆150Updated this week
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆109Jun 2, 2026Updated 3 months ago
- Locus and lineage tests for bacterial GWAS☆28Oct 5, 2017Updated 8 years ago
- a short-read polishing tool for long-read assemblies☆224Jul 28, 2026Updated last month
- Recombination-free trees☆72Jul 24, 2026Updated last month
- Finding regions of similarity between plasmids☆17Jul 15, 2026Updated last month
- SEER, reimplemented in python 🐍🔮☆138Jul 23, 2026Updated last month
- Antimicrobial Resistance Identification By Assembly☆186Oct 12, 2023Updated 2 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Identify phage regions in bacterial genomes for masking purposes☆33Sep 5, 2019Updated 6 years ago
- Rapid determination of appropriate reference genomes.☆103Jan 22, 2025Updated last year
- Split k-mer analysis – version 2☆105Jul 9, 2026Updated last month
- A tool for removing redundant genomes from a set of assemblies☆85Jul 24, 2026Updated last month
- A toolbox for pangenome analysis and threshold evaluation.☆101Jul 8, 2022Updated 4 years ago
- A flexible pipeline for complete analysis of bacterial genomes☆523Aug 5, 2026Updated 3 weeks ago
- Mass screening of contigs for antimicrobial and virulence genes☆507Jul 17, 2026Updated last month
- Pipeline for analysing intergenic regions in bacteria☆39Oct 25, 2019Updated 6 years ago
- AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and p…☆388Updated this week
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆50May 18, 2026Updated 3 months ago
- Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.☆206Jun 10, 2026Updated 2 months ago
- An updated pipeline for pangenome investigation☆374Jul 2, 2026Updated 2 months ago
- Genome size estimation from long read overlaps☆92Updated this week
- MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies☆183Apr 16, 2025Updated last year
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆28Sep 7, 2019Updated 6 years ago
- Making whole bacterial genome sequencing data analysis easy☆115Apr 22, 2025Updated last year