Pairwise SNP distance matrix from a FASTA sequence alignment
☆157Dec 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☆593Dec 12, 2025Updated 9 months ago
- Pan-genome wide association studies☆226May 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 7 months ago
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆127Jun 2, 2026Updated 3 months 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.
- Create a tree using Mash distances☆190Oct 24, 2023Updated 2 years ago
- Finds SNP sites from a multi-FASTA alignment file☆280Dec 16, 2020Updated 5 years ago
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins☆225Aug 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☆145Dec 9, 2025Updated 9 months ago
- Scan contig files against PubMLST typing schemes☆302Jun 17, 2026Updated 3 months ago
- ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads☆268Jun 11, 2026Updated 3 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…☆158Sep 2, 2026Updated 3 weeks ago
- Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment☆16Dec 5, 2018Updated 7 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.
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆99Dec 9, 2025Updated 9 months ago
- BSR-Based Allele Calling Algorithm☆151Sep 17, 2026Updated last week
- PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)☆112Jun 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☆226Jul 28, 2026Updated last month
- Recombination-free trees☆73Jul 24, 2026Updated 2 months ago
- Finding regions of similarity between plasmids☆17Jul 15, 2026Updated 2 months ago
- SEER, reimplemented in python 🐍🔮☆138Jul 23, 2026Updated 2 months ago
- Antimicrobial Resistance Identification By Assembly☆187Oct 12, 2023Updated 2 years ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Identify phage regions in bacterial genomes for masking purposes☆33Sep 5, 2019Updated 7 years ago
- Rapid determination of appropriate reference genomes.☆104Jan 22, 2025Updated last year
- Split k-mer analysis – version 2☆106Jul 9, 2026Updated 2 months ago
- A tool for removing redundant genomes from a set of assemblies☆86Jul 24, 2026Updated 2 months ago
- A toolbox for pangenome analysis and threshold evaluation.☆102Jul 8, 2022Updated 4 years ago
- A flexible pipeline for complete analysis of bacterial genomes☆522Aug 5, 2026Updated last month
- Mass screening of contigs for antimicrobial and virulence genes☆512Jul 17, 2026Updated 2 months ago
- 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…☆391Aug 31, 2026Updated 3 weeks ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf☆50Sep 4, 2026Updated 2 weeks ago
- Genome size estimation from long read overlaps☆97Sep 8, 2026Updated 2 weeks ago
- Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.☆208Jun 10, 2026Updated 3 months ago
- An updated pipeline for pangenome investigation☆377Jul 2, 2026Updated 2 months ago
- MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies☆184Apr 16, 2025Updated last year
- 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies☆28Sep 7, 2019Updated 7 years ago
- Making whole bacterial genome sequencing data analysis easy☆116Apr 22, 2025Updated last year