Finds SNP sites from a multi-FASTA alignment file
☆278Dec 16, 2020Updated 5 years ago
Alternatives and similar repositories for snp-sites
Users that are interested in snp-sites are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Pairwise SNP distance matrix from a FASTA sequence alignment☆156Dec 31, 2025Updated 7 months ago
- Rapid haploid variant calling and core genome alignment☆595Dec 12, 2025Updated 8 months ago
- ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads☆264Jun 11, 2026Updated 2 months ago
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins☆221Aug 27, 2025Updated 11 months ago
- A tool to circularize genome assemblies☆257Apr 6, 2024Updated 2 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.
- Antimicrobial Resistance Identification By Assembly☆186Oct 12, 2023Updated 2 years ago
- Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction☆253Updated this week
- Pan-genome wide association studies☆224May 29, 2024Updated 2 years ago
- Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data☆119Aug 21, 2023Updated 2 years ago
- Mummer alignment tool☆571Feb 4, 2025Updated last year
- "Reads to report" for public health and clinical microbiology☆144Dec 9, 2025Updated 8 months ago
- Rapid large-scale prokaryote pan genome analysis☆380Nov 3, 2025Updated 9 months ago
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆127Jun 2, 2026Updated 2 months ago
- In-depth characterization and annotation of differences between two sets of DNA sequences☆64May 18, 2020Updated 6 years 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.
- An updated pipeline for pangenome investigation☆370Jul 2, 2026Updated last month
- 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…☆157Oct 2, 2025Updated 10 months ago
- Fast genome and metagenome distance estimation using MinHash☆451Sep 19, 2025Updated 10 months ago
- A fast approximate aligner for long DNA sequences☆289Oct 11, 2024Updated last year
- Scan contig files against PubMLST typing schemes☆297Jun 17, 2026Updated 2 months ago
- Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets☆214Aug 21, 2024Updated last year
- Mass screening of contigs for antimicrobial and virulence genes☆507Jul 17, 2026Updated last month
- Rapid prokaryotic genome annotation☆992Jan 6, 2026Updated 7 months ago
- SPAdes Genome Assembler☆955Jun 16, 2026Updated 2 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.
- Scripts to download genomes from the NCBI FTP servers☆1,083Apr 7, 2026Updated 4 months ago
- Create a tree using Mash distances☆189Oct 24, 2023Updated 2 years ago
- Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr…☆301May 9, 2024Updated 2 years ago
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆666Aug 7, 2026Updated last week
- Ultrafast Sample Placement on Existing Trees☆140Jun 1, 2026Updated 2 months ago
- Genome assembly evaluation tool☆518Jun 10, 2026Updated 2 months ago
- NCBI Pathogen Detection Portal toolkit☆11Sep 6, 2023Updated 2 years ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Feb 15, 2019Updated 7 years ago
- Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment☆16Dec 5, 2018Updated 7 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.
- In silico prediction of E. coli serotype, pathotype and shiga toxin subtyping☆66Jun 5, 2025Updated last year
- C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings☆683Mar 20, 2026Updated 4 months ago
- hybrid assembly pipeline for bacterial genomes☆650Jul 29, 2026Updated 3 weeks ago
- A set of scripts for calculating pairwise SNP distance☆45Feb 19, 2026Updated 6 months ago
- Chromosome-level scaffolding using multiple references☆170Sep 8, 2024Updated last year
- A resistome profiler for Graphing Resistance Out Of meTagenomes☆65May 11, 2020Updated 6 years ago
- Rapid determination of appropriate reference genomes.☆103Jan 22, 2025Updated last year