Efficient phylogenetic clustering of viral sequences
☆100Nov 19, 2025Updated 8 months ago
Alternatives and similar repositories for TreeCluster
Users that are interested in TreeCluster are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Phylogenetic Clustering by Linear Integer Programming (PhyCLIP)☆19Oct 27, 2020Updated 5 years ago
- For all your cluster needs☆18Feb 3, 2023Updated 3 years ago
- Reference-guided multiple sequence alignment of viral genomes☆73May 30, 2026Updated last month
- A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment☆20Nov 12, 2025Updated 8 months ago
- Efficient phylogenetic tree inference for massive taxonomic datasets☆147Apr 6, 2025Updated last year
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- ☆18Oct 7, 2024Updated last year
- Inferring global and local strict molecular clocks using root-to-tip regression☆20Jun 30, 2026Updated 3 weeks ago
- Fast viral consensus genome reconstruction☆27Jun 19, 2026Updated last month
- CLI tool for querying the Genome Taxonomy Database (GTDB). Batch search, genome cards, taxon lineages, and cross-release taxonomic compar…☆31Updated this week
- A message queue for genomic surveillance☆20Oct 14, 2021Updated 4 years ago
- In silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis☆16Feb 19, 2026Updated 5 months ago
- app to collapse Pango lineages for reporting☆13Dec 9, 2025Updated 7 months ago
- Bin Chicken - recovery of low abundance and taxonomically targeted metagenome assembled genomes (MAGs) through strategic coassembly☆77Jul 13, 2026Updated last week
- Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!☆189Mar 17, 2026Updated 4 months ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- snipit: summarise snps relative to your reference sequence☆178Jan 13, 2026Updated 6 months ago
- A tool for the identification of coincident (associating and dissociating) genes in pangenomes.☆112Oct 20, 2023Updated 2 years ago
- A hybrid assembly and MAG recovery pipeline (and more!)☆110Updated this week
- strain-level analysis tools☆41Oct 21, 2024Updated last year
- Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.☆54Mar 23, 2026Updated 4 months ago
- Utility to alias and dealias pango lineages☆23Dec 18, 2023Updated 2 years ago
- 🦠🧬🧑💻📇 Microbial genomes-to-report pipeline☆75Mar 14, 2026Updated 4 months ago
- 🦠🧬 Unraveling Viral Genomes from Metagenomes☆11Oct 3, 2025Updated 9 months ago
- Fast and accurate tool for calculating Average Nucleotide Identity (ANI) and clustering virus genomes and metagenomes☆110Jul 7, 2026Updated 2 weeks 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.
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Jun 9, 2026Updated last month
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆20Dec 3, 2024Updated last year
- interactive barplot for amplicon sequencing☆13Dec 5, 2024Updated last year
- Pipeline for analysing intergenic regions in bacteria☆39Oct 25, 2019Updated 6 years ago
- NCBI-style taxdump files for International Committee on Taxonomy of Viruses (ICTV)☆22May 3, 2025Updated last year
- Official place for proposals and details around monkeypox virus lineage designations☆23Jul 7, 2026Updated 2 weeks ago
- A toolbox for pangenome analysis and threshold evaluation.☆101Jul 8, 2022Updated 4 years ago
- ☆22Feb 12, 2026Updated 5 months ago
- ☆13Aug 15, 2025Updated 11 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.
- Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.☆259May 13, 2026Updated 2 months ago
- Resolving Species Level Classification Using Emu☆14Jun 14, 2024Updated 2 years ago
- Plasmid analysis using rearrangement distances☆56Updated this week
- ccfind - circular complete genome finder with clues of terminal redundancy☆16Mar 5, 2026Updated 4 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…☆157Oct 2, 2025Updated 9 months ago
- Create a tree using Mash distances☆188Oct 24, 2023Updated 2 years ago
- Reconstruction and analysis of viral and host genomes at multi-organ level☆21Apr 10, 2026Updated 3 months ago