Python and Rust library for loading, saving, and manipulating taxonomic trees
☆54Jun 22, 2026Updated 2 months ago
Alternatives and similar repositories for taxonomy
Users that are interested in taxonomy are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- HyGen: Compact and Efficient Genome Sketching using Hyperdimensional Vectors☆33Aug 26, 2024Updated 2 years ago
- A genomic minhashing implementation in Rust☆101Jul 8, 2026Updated last month
- ☆14Oct 14, 2020Updated 5 years ago
- Experiments with using BIGSI data structure for metagenomic and QC applications☆19Aug 12, 2024Updated 2 years ago
- Simple Python interface to CoverM's fast coverage estimation functions☆11Dec 20, 2024Updated last year
- 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.
- Fast FASTX parsing and k-mer methods in Rust☆214Jun 22, 2026Updated 2 months ago
- Bitpacked sequence trait and implementation☆19Aug 19, 2026Updated last week
- Fast and Memory Efficient Genome Sketching via HyperLogLog, HyperMinHash, UltraLogLog and ExaLogLog☆22Aug 19, 2026Updated last week
- ☆20Jan 13, 2026Updated 7 months ago
- k-mers and the like☆23Aug 9, 2026Updated 3 weeks ago
- Taxonomy classification of viral sequences / contigs☆13Jul 15, 2025Updated last year
- A Python package for obtaining, parsing and exploring biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)☆52May 5, 2026Updated 3 months ago
- Iterate over minimizers of a DNA sequence☆33Jul 12, 2024Updated 2 years ago
- A SIMD-accelerated library to compute random minimizers☆46Updated this week
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Compute bottom-s sketches and s-buckets sketches, using simd-minimizers crate.☆21Updated this week
- ntHash implementation in Rust☆36Jul 12, 2024Updated 2 years ago
- Host depletion optimised for clinical metagenomic sequencing applications☆19Jul 9, 2026Updated last month
- Minimum plain text representation of kmer sets☆18Jan 30, 2025Updated last year
- Rust bindings to minimap2 library☆113May 3, 2026Updated 3 months ago
- syncmer graphs, and perhaps other sorts of sequence graphs☆44Updated this week
- Make phylogenetic trees and lineages from the NCBI Taxonomy database☆14Mar 19, 2023Updated 3 years ago
- A versatile toolkit for k-mers with taxonomic information☆85Aug 28, 2025Updated last year
- An extensible and performant aligner and read mapper☆103Jul 27, 2026Updated last month
- 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.
- Extremely fast and accurate Nanopore demultiplexing☆106Jul 18, 2026Updated last month
- A Go implementation of the strobemers (https://github.com/ksahlin/strobemers)☆14Apr 23, 2021Updated 5 years ago
- VariantStore: A Large-Scale Genomic Variant Search Index☆40Jul 9, 2021Updated 5 years ago
- fast, multithreaded sourmash operations: search, compare, and gather.☆26Aug 10, 2026Updated 2 weeks ago
- Tearing through FASTA/Q sequences☆38Jul 9, 2026Updated last month
- Fasten toolkit, for streaming operations on fastq files☆82Oct 24, 2025Updated 10 months ago
- Compute a pairwise SNP distance matrix from one or two alignment(s)☆27Sep 12, 2024Updated last year
- Chimera: A Versatile Metagenomic Classification Tool☆21Aug 16, 2026Updated 2 weeks ago
- sunburst plots for taxonomy - working to update Krona☆46Sep 22, 2025Updated 11 months ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- String algorithm visualizations☆14Feb 7, 2023Updated 3 years ago
- Fast approximate string searching☆164Aug 11, 2026Updated 2 weeks ago
- Build sourmash databases for genbank.☆10May 4, 2023Updated 3 years ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆70Apr 10, 2025Updated last year
- Fast, parallel Rust implementation of Prodigal for prokaryotic gene prediction in microbial genomes☆29Jul 26, 2026Updated last month
- COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)☆22Nov 24, 2024Updated last year
- Strain resolver for metagenomics☆82Aug 2, 2024Updated 2 years ago