External directory
Tools we don’t host, indexed because they are the right answer to something. Every entry says when to reach for it, what it costs you in access or licensing, and what to use instead when it isn’t the right fit.
Molecular biology
- Primer3
The reference primer design engine, still the one to beat.
ExternalWhitehead InstituteFree - Primer-BLAST
Primer design with a specificity check against a whole genome.
ExternalNCBIFree - NEBcutter
Restriction mapping and digest planning against a real enzyme catalogue.
ExternalNew England BiolabsFree - Benchling
Cloud plasmid editor and lab notebook, free for academic use.
ExternalBenchlingFree tier - SnapGene Viewer
Free viewer for annotated plasmid maps and sequence files.
ExternalDotmaticsDesktop install - CHOPCHOP
CRISPR guide RNA design with off-target scoring.
ExternalUniversity of BergenFree
Bioinformatics
- NCBI BLAST
Similarity search against every public sequence database.
ExternalNCBIFree - Clustal Omega
Multiple sequence alignment that scales to thousands of sequences.
ExternalEMBL-EBIFree - MAFFT
Multiple alignment with accuracy modes for difficult sequence sets.
ExternalEMBL-EBIFree - EMBOSS Needle
Global pairwise alignment, the reference implementation.
ExternalEMBL-EBIFree - UniProt
The reference protein sequence and functional annotation database.
ExternalEMBL-EBI / SIB / PIRFree - InterPro
Protein family, domain and functional site annotation in one place.
ExternalEMBL-EBIFree - Ensembl
Genome browser with comparative genomics and variation data.
ExternalEMBL-EBIFree
Protein tools
- AlphaFold Server
Predicts protein, DNA, RNA and ligand complexes with AlphaFold 3.
ExternalGoogle DeepMindSign-in - ColabFold
AlphaFold2 and multimer predictions in a notebook, with no local GPU.
ExternalSteinegger & MirditaFree - I-TASSER
Threading-based modelling with function and ligand-site prediction.
ExternalZhang LabSign-in - CHARMM-GUI
Builds ready-to-run input files for molecular dynamics simulations.
ExternalLehigh UniversitySign-in - Mol* Viewer
Fast 3D structure viewing in the browser; the PDB default.
ExternalRCSB PDB / PDBeFree - RCSB PDB
The Protein Data Bank: every experimentally determined structure.
ExternalRCSBFree
Cell biology
Imaging & microscopy
- Fiji / ImageJ
The standard for scientific image analysis, with a plugin for almost everything.
ExternalOpen sourceDesktop install - CellProfiler
High-throughput image analysis pipelines without writing code.
ExternalBroad InstituteFree - napari
Multidimensional image viewer built for Python workflows.
ExternalOpen sourceDesktop install - QuPath
Whole-slide and digital pathology image analysis.
ExternalUniversity of EdinburghDesktop install