bioinformatics

Inference of ploidy and heterozygosity structure using whole genome sequencing data

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

Source code for JBrowse 2, a modern React-based genome browser

GCP for Bioinformatics Researchers

Python package to perform enrichment analysis from omics data.

Python library to parse, format, validate, normalize, and map sequence variants according to HGVS Nomenclature (https://hgvs-nomenclature.org/).

minimal example implementations for bioinformatics workflow managers

Plant Disease Identification Using Convulutional Neural Network

Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling asses...

Reads simulator

Python library for array programming on biological datasets. Documentation available at: https://bionumpy.github.io/bionumpy/

ECG classification programs based on ML/DL methods

UGENE is free open-source cross-platform bioinformatics software

🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.

Multiple Protein Structure Alignment at Scale with FoldMason

Versatile computational pipeline for processing protein structure data for deep learning applications.

:pencil2: A versatile DNA sequence optimizer

Finds SNP sites from a multi-FASTA alignment file

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downlo...

Reusable genomic evidence for research and analysis tools: exact read evidence, portable datasets, and managed analyzers.

[ICML 2026] Autonomous AI agent for end-to-end spatial proteomics analysis, with SP-Bench for agentic multiplexed-imaging workflows.

Official repo of the modular BioExcel version of HADDOCK

Tutorial for scRNA-seq data analysis beginners using R

UCSC Genome Browser source. "beta" is released version / "master" is testing.

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

Ultra-deep search for novel viruses

WebAssembly modules for genomics

Syntax highlighting for computational biology

:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial com...

Randomly subsample sequencing reads or alignments

Robs manual for the computational genomics and bioinformatics class.

GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms...

Algorithm for ultra-scale multiple protein sequence alignments: 3 million ABC transporters analyzed in 5 minutes and 18 GB of RAM.

HyPhy: Hypothesis testing using Phylogenies

A powerful open source data warehouse system

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of t...

Github for files currently published in the IPD-IMGT/HLA FTP Directory hosted at the European Bioinformatics Institute

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

An ultrafast memory-efficient short read aligner

Python for Bioinformatics

A Python frontend to (Open Biomedical) Ontologies.

A genome completeness evaluation tool based on miniprot

DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.

Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.

Awesome-Biomolecule-Language-Cross-Modeling: a curated list of resources for paper "Leveraging Biomolecule and Natural Language through Multi-Modal Le...

A tool to circularize genome assemblies

Deep learning infrastructure for genomics

Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal

Cuneiform distributed programming language