☆18Jun 11, 2024Updated 2 years ago
Alternatives and similar repositories for CaveDive
Users that are interested in CaveDive are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Disty McMatrixface - compute a distance matrix from a core genome alignment file☆15Mar 15, 2023Updated 3 years ago
- ☆23Jul 5, 2026Updated 2 weeks ago
- Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and MTB classification☆14Apr 8, 2024Updated 2 years ago
- ☆12Updated this week
- in silico typing of the H. influenzae cap locus☆13Jul 15, 2024Updated 2 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.
- Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)☆41Apr 17, 2024Updated 2 years ago
- Scalable relaxed clock phylogenetic dating☆28Jul 5, 2026Updated 2 weeks ago
- Quality control for phylogenetic analyses☆13Jul 13, 2026Updated last week
- SpydrPick: mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.☆16Apr 29, 2022Updated 4 years ago
- A tool to identify and annotate homoplasies on a phylogeny and sequence alignment☆24Jun 2, 2021Updated 5 years ago
- ☆15Mar 17, 2026Updated 4 months ago
- R integration for edlib, a C/C++ library for pairwise sequence alignment using edit distance (Levenshtein distance).☆11Jul 20, 2025Updated last year
- Evaluating Nanopore-based bacterial variant calling☆23Jul 23, 2025Updated last year
- For bluntifying overlapped GFAs☆13Jul 26, 2024Updated last year
- 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.
- Goalign : a set of command line tools and an API to manipulate multiple sequence alignments.☆90Jul 15, 2026Updated last week
- Coalescent simulation and likelihood for phylodynamic inference☆16May 15, 2025Updated last year
- Library of sketching functions used by PopPUNK☆31Jun 8, 2026Updated last month
- Recombination-free trees☆72Updated this week
- Assort phage protein sequences into phamilies using MMseqs2☆12Dec 16, 2024Updated last year
- Ultrafast Sample Placement on Existing Trees☆140Jun 1, 2026Updated last month
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆48Jun 19, 2026Updated last month
- A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data☆71Feb 23, 2026Updated 5 months ago
- Inferring spatiotemporal dynamics of H5N1 influenza from sequence data☆10Sep 6, 2013Updated 12 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.
- ProphAsm – a rapid computation of simplitigs directly from k-mer sets☆25Feb 17, 2023Updated 3 years ago
- Phylotype your strains using Clermont's 2013 method: ezclermont.org☆16May 5, 2026Updated 2 months ago
- app to collapse Pango lineages for reporting☆13Dec 9, 2025Updated 7 months ago
- Miscellaneous Perl scripts from 20 years in microbial bioinformatics☆18Jul 16, 2024Updated 2 years ago
- HyLight is a strain aware de novo assembly method based on the overlap-layout-consensus (OLC) paradigm that leverages the strengths of NG…☆12Sep 18, 2024Updated last year
- Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories☆40Feb 20, 2026Updated 5 months ago
- Rapid discovery of reciprocal best blast pairs.☆10Nov 9, 2024Updated last year
- A tooL for Prokaryotic Phylogeny And Clustering Analysis☆14May 22, 2026Updated 2 months ago
- NCBI Pathogen Detection Portal toolkit☆11Sep 6, 2023Updated 2 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.
- Implementation of the treeSeg algorithm as an R package.☆14Feb 2, 2026Updated 5 months ago
- Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI☆29Dec 4, 2018Updated 7 years ago
- Genomic neighbor typing of bacterial pathogens using MinHash☆42Jan 10, 2023Updated 3 years ago
- Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction☆254Updated this week
- snipit: summarise snps relative to your reference sequence☆178Jan 13, 2026Updated 6 months ago
- Phylogenetic maximum representation sampling: choosing most representative strains or taxa☆42Jul 2, 2026Updated 3 weeks ago
- Prokaryotic Pangenome Analysis☆24Dec 3, 2021Updated 4 years ago