- CloneIt
 - An online programme finding sub-cloning strategies, in-frame deletions, and frameshifts using restriction enzymes and DNA polymerases. - NEBcutter
- Online DNA restriction mapping tool.
- REBASE Digest
- Online tool which takes a DNA sequence and digests it with one example of each of the known Type 2 restriction enzyme specificities.
- REBASE: The Restriction Enzyme Database
- Collection of information about restriction enzymes, methylases, the microorganisms from which they have been isolated, recognition sequences, cleavage sites, methylation specificity, the commercial availability of the enzymes, and references.
- Restriction Enzyme Analysis
- Identifies restriction mapping sites in DNA sequences.
- Restriction Mapper
- Finds restriction endonuclease cleavage sites in DNA sequences. Supports linear and circular DNA and provides several ways to sort and filter output.
- WatCut
- Online restriction mapping, silent mutagenesis, and mutagenic primer design for SNP genotyping by restriction analysis.
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