Python and Rust library for loading, saving, and manipulating taxonomic trees
☆53Mar 15, 2026Updated this week
Alternatives and similar repositories for taxonomy
Users that are interested in taxonomy are comparing it to the libraries listed below
Sorting:
- HyGen: Compact and Efficient Genome Sketching using Hyperdimensional Vectors☆30Aug 26, 2024Updated last year
- ☆14Oct 14, 2020Updated 5 years ago
- A genomic minhashing implementation in Rust☆103Jun 17, 2025Updated 9 months ago
- Bitpacked sequence trait and implementation☆16Feb 27, 2026Updated 3 weeks ago
- Simple Python interface to CoverM's fast coverage estimation functions☆10Dec 20, 2024Updated last year
- Fast FASTX parsing and k-mer methods in Rust☆210Jan 27, 2026Updated last month
- A SIMD-accelerated library to compute random minimizers☆39Mar 1, 2026Updated 2 weeks ago
- k-mers and the like☆22Mar 2, 2026Updated 2 weeks ago
- Taxonomy classification of viral sequences / contigs☆12Jul 15, 2025Updated 8 months ago
- A Python package for obtaining, parsing and exploring biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)☆48Feb 5, 2026Updated last month
- Iterate over minimizers of a DNA sequence☆32Jul 12, 2024Updated last year
- Compute bottom-s sketches and s-buckets sketches, using simd-minimizers crate.☆21Dec 3, 2025Updated 3 months ago
- Minimum plain text representation of kmer sets☆16Jan 30, 2025Updated last year
- ntHash implementation in Rust☆36Jul 12, 2024Updated last year
- Fast and Memory Efficient Genome Sketching via HyperLogLog, HyperMinHash and UltraLogLog☆20Jan 22, 2026Updated last month
- Rust bindings to minimap2 library☆109Mar 2, 2026Updated 2 weeks ago
- Experiments with using BIGSI data structure for metagenomic and QC applications☆19Aug 12, 2024Updated last year
- 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☆82Aug 28, 2025Updated 6 months ago
- sunburst plots for taxonomy - working to update Krona☆44Sep 22, 2025Updated 5 months ago
- A Go implementation of the strobemers (https://github.com/ksahlin/strobemers)☆14Apr 23, 2021Updated 4 years ago
- VariantStore: A Large-Scale Genomic Variant Search Index☆39Jul 9, 2021Updated 4 years ago
- fast, multithreaded sourmash operations: search, compare, and gather.☆25Updated this week
- Compute a pairwise SNP distance matrix from one or two alignment(s)☆26Sep 12, 2024Updated last year
- Fasten toolkit, for streaming operations on fastq files☆81Oct 24, 2025Updated 4 months ago
- ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.☆298Feb 3, 2026Updated last month
- Build sourmash databases for genbank.☆11May 4, 2023Updated 2 years ago
- Chimera: A Versatile Metagenomic Classification Tool☆21Feb 1, 2026Updated last month
- COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)☆20Nov 24, 2024Updated last year
- String algorithm visualizations☆13Feb 7, 2023Updated 3 years ago
- A database for signatures of public genomic sources☆18Jan 1, 2026Updated 2 months ago
- More scalable dereplication for metagenome assembled genomes☆78Mar 8, 2026Updated last week
- Automatically build wheels for packages released on PyPI☆15Nov 25, 2019Updated 6 years ago
- Simple succinct data structures (in Rust)☆54Feb 12, 2026Updated last month
- genome_updater is a bash script that downloads and updates (non-redundant) snapshots of the NCBI Genomes repository (RefSeq/GenBank) with…☆168Mar 12, 2026Updated last week
- SIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using …☆139Jun 23, 2024Updated last year
- A novel method for sequence similarity estimation☆28Mar 23, 2024Updated last year
- Fast approximate string searching☆106Mar 13, 2026Updated last week
- An ultrafast and memory efficient tool for phylogenomics☆26Jan 31, 2026Updated last month