bioinformatics

ECG classification programs based on ML/DL methods

Reads simulator

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

Plant Disease Identification Using Convulutional Neural Network

Multiple Protein Structure Alignment at Scale with FoldMason

197 bioinformatics & life science skills for Claude Code and AI agents — BixBench 92.0% accuracy. RNA-seq, single-cell, drug discovery, proteomics, an...

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

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

Finds SNP sites from a multi-FASTA alignment file

UGENE is free open-source cross-platform bioinformatics software

:pencil2: A versatile DNA sequence optimizer

Ultra-deep search for novel viruses

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

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

Syntax highlighting for computational biology

Tutorial for scRNA-seq data analysis beginners using R

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

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

A powerful open source data warehouse system

Robs manual for the computational genomics and bioinformatics class.

WebAssembly modules for genomics

Randomly subsample sequencing reads or alignments

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...

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

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

An ultrafast memory-efficient short read aligner

Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)

HyPhy: Hypothesis testing using Phylogenies

A Python frontend to (Open Biomedical) Ontologies.

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

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

Python for Bioinformatics

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

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

Deep learning infrastructure for genomics

A tool to circularize genome assemblies

Official repo of the modular BioExcel version of HADDOCK

A genome completeness evaluation tool based on miniprot

Deterministic, resource-governed per-locus genomics analyses with transactional artifacts, receipts, replay, Arrow, and reproducible sharding.

Cuneiform distributed programming language

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

Tools for manipulating sequence graphs in the GFA and rGFA formats

Download sequencing data and metadata from GSA, SRA, ENA, and DDBJ databases.

Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal

📚 Tools and databases for analyzing HLA and VDJ genes.

A cool place to store your Hi-C

Next generation sequencing reads de novo assembler.

A curated list of resources for machine learning for small-molecule drug discovery

Pegasus Workflow Management System - Automate, recover, and debug scientific computations.