AlphaFold is an open‑source deep learning system for high‑accuracy protein structure prediction (monomers and multimers), producing ranked PDB models with per‑residue confidence (pLDDT), PAE/pTM estimates and machine‑readable outputs for downstream analysis.
AlphaFold DB is an open-access repository of AlphaFold protein structure predictions—over 200 million models from DeepMind and EMBL‑EBI—providing downloadable PDB/mmCIF coordinates, per-residue confidence (pLDDT), PAE, and bulk search/download tools.
anndata is a Python library for storing and manipulating annotated data matrices (especially single‑cell omics) in memory and on disk, with sparse data support, lazy operations, Dask/Zarr backends and a PyTorch interface.
Antha (Synthace) is a laboratory automation and experimental design platform that converts complex biological workflows and multifactorial DOE into reproducible, automated protocols—speeding assay development and discovery.
Apache Airflow is an open-source platform to programmatically author, schedule, and monitor workflows as Python DAGs — providing a scalable scheduler, rich UI, operators for cloud/services, and an extensible provider ecosystem for ETL, MLOps, and infra automation.
ApE (A Plasmid Editor) is a lightweight, donation-supported sequence editor for designing, annotating and analyzing DNA constructs—featuring restriction maps, primer design, trace alignment, assembly wizards and rich import/export support.
Argo Workflows is an open-source, Kubernetes-native workflow engine (CRD) that orchestrates containerized, parallel jobs using DAG or step-based specs—ideal for CI/CD, ML training, data processing and large-scale batch workloads.
AUGUSTUS is an open-source eukaryotic gene prediction tool that uses a generalized Hidden Markov Model and external evidence (ESTs, proteins, RNA‑Seq, comparative alignments) to produce accurate gene structures, UTRs and alternative transcripts.
Basenji is an open-source toolkit that trains deep convolutional neural networks on chromosome-scale DNA to predict quantitative regulatory activity, score variants (SAD/SED), and map distal regulatory elements and nucleotide drivers.
BBTools is a fast, Java-based, open-source suite for preprocessing and analysing high-throughput sequencing data — offering read trimming, contamination filtering, mapping, error correction and k-mer tools to streamline NGS workflows.
BCFtools is a command‑line suite for calling, manipulating, filtering and annotating variants in VCF/BCF/gVCF formats. It’s designed for streaming pipelines, works with bgzip/tabix indexes, and integrates tightly with samtools/HTSlib for reproducible genomic workflows.
BEDTools is a fast, open-source toolkit for genome “arithmetic” — set operations on genomic intervals — enabling intersections, merges, coverage, proximity queries and other interval manipulations across common genomics formats.
