Bioinformatics software
- .NET Bio
- AlleleID
- AlphaFold
- AMAP
- Anduril (workflow engine)
- ANGIS
- ANNOVAR
- Apache Taverna
- ArrayTrack
- Beacon designer
- Bellerophon program
- BioBIKE
- BioCompute Object
- Bioinformatics workflow management system
- Bioinformatic Harvester
- BioJava
- BioLinux
- BioMart
- BioNumerics
- Biopython
- BioSLAX
- BLAT (bioinformatics)
- Broadly neutralizing HIV-1 antibodies
- Budapest Reference Connectome
- Chemistry Development Kit
- CheShift
- Clone manager
- CloudBioLinux
- Cn3D
- COMPLEAT (Bioinformatics tool)
- Computational Resource for Drug Discovery
- CS-BLAST
- Cytoscape
- DAVID
- Debian-Med
- DNADynamo
- DreamLab
- DTA GView
- EMBOSS
- EMovie
- Empire (program)
- EsyN
- ETBLAST
- Eurocarbdb
- FlowJo
- FlyExpress
- Formatdb
- Galaxy (computational biology)
- GeneMark
- GeneNetwork
- GenePattern
- Generic Model Organism Database
- GENESIS (software)
- Genevestigator
- GenGIS
- GenMAPP
- GENSCAN
- GENtle
- Geworkbench
- HH-suite
- HMMER
- IMOD (software)
- Integromics
- InterMine
- IntFOLD
- Intrinsic Noise Analyzer
- Kepler scientific workflow system
- KiSAO
- List of systems biology modeling software
- MacVector
- Mascot (software)
- Mass spectrometry data format
- MEME suite
- Metascape
- MochiView
- Molecular Evolutionary Genetics Analysis
- MolIDE
- Morphobank
- MUMmer
- Newbler
- OLIGO Primer Analysis Software
- OpenChrom
- OpenMS
- OrthoFinder
- Osteoware
- ParaSurf
- Pathway analysis
- PatternHunter
- PhagesDB
- Phrap
- Phred (software)
- Phyre
- PICRUSt
- Pipeline Pilot
- PLINK (genetic tool-set)
- Primer Premier
- Protein subcellular localization prediction
- Proteomics Standards Initiative
- ProteoWizard
- PSORT
- QIIME
- Qlucore
- Rosalind (education platform)
- Rosetta@home
- SAAM II
- Sequence profiling tool
- Sequerome
- Sequest
- Skyline (software)
- Snagger (software)
- SOSUI
- Staden Package
- Stemloc
- TaveRNA
- The Proteolysis Map
- TimeTree
- TopFIND
- Trans-Proteomic Pipeline
- Ubuntu-Med
- UTOPIA (bioinformatics tools)
- Vector NTI
- Viral Bioinformatics Resource Center
- WHAT IF software
- XCMS Online
- Xrate
- List of open-source bioinformatics software
- DICOM software
- Lists of bioinformatics software
- Metagenomics software
- Phylogenetics software
- Structural bioinformatics software
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