Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

A better and stronger spiritual successor to BZip2.

HyPhy: Hypothesis testing using Phylogenies

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV

PanPA is a tool for building panproteome graphs and aligning sequences back to the graphs.

Fast and memory-efficient exact attention

The best ChatGPT that $100 can buy.

BBTools: Official suite of fast, multithreaded bioinformatics tools for DNA/RNA analysis. BBMap aligner, BBDuk trimmer, BBMerge, and 90+ other tools. Actively maintained by Brian Bushnell.

BUSCO Phylogenomics | Utility script to construct species phylogenies using BUSCO proteins

Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.

Demonstration of AI review of existing functional annotations

family tree visualization built on top of d3

🚀 LiftOn: Accurate annotation mapping for GFF/GTF across assemblies

Scripts to build high-quality genome-scale metabolic model by using a deep neural network to guide gapfilling

Open source comprehensive 2D content creation tool suite for graphic design, digital art, and interactive real-time motion graphics — featuring node-based procedural editing

A Python toolkit for biomedical data integration and harmonization

kira-cdh is a single-binary, CLI-compatible replacement for the core CD-HIT utilities

A high-performance, lock-free concurrent cuckoo filter implementation in Rust

Infering ancestral synteny with hierarchical orthologous groups

A simple registry for KGHub projects

Code for 'LLM2Vec: Large Language Models Are Secretly Powerful Text Encoders'

EnzyMM - Enzyme Motif Miner - Geometric matching of catalytic motifs in protein structures.

Demonstration of AI review of existing functional annotations

GraphPart, a data partitioning method for ML on biological sequences

A small gui app for Linux to control the fan speed and monitor temps on a ThinkPad

A beautiful, non-destructive, and GPU-accelerated RAW image editor built with performance in mind.

A Python library for extracting structured information from unstructured text using LLMs with precise source grounding and interactive visualization.

Sunburst representation of ontologies