- Argo Genome Browser
- Free, open source production tool used in visualizing and manually annotating whole genomes.
- DNADynamo
- Sequence analysis software particularly designed for molecular biologists.
- EMBOSS
- European Molecular Biology Open Software Suite – a free online software analysis package specially developed for molecular biology.
- EnzymeX
- Program developed to help molecular biologists in determining which restriction enzymes to use to cut a DNA of interest.
- Insilico Biotechnology
- Predicts and optimizes cellular processes for the life sciences industries through the creation of computational models of living cells.
- JaMBW 1.1
- Java based molecular biologist's "workbench" available as a free online tool.
- MacVector, Inc.
- Developer of easy-to-use Macintosh applications that help molecular biologists in analyzing, assembling, and documenting DNA and protein sequences.
- Sequentix
- Offers software and professional services for DNA analysis. With news, references, and contact details.
- SoftZymics
- Specializes in developing software for enzymology or enzyme kinetics.
- StarBiochem
- Application enabling users to explore fundamental biological research concepts, select parts of molecules, and control how such selected parts are displayed.
- Textco BioSoftware
- Maker of molecular biology software offering applications for gene construction and inspection, desktop cloning, DNA analysis, and protein analysis.
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