Molecular cloning

Comprehensive in silico cloning functionality. Illustrate your templates and vectors with automatic annotations.

Automatically annotate plasmid maps and expression vectors

Geneious Prime is connected to PlasMapper which allows you to automatically highlight plasmids with common promoters, terminators, cloning sites, restriction sites, reporter genes, affinity tags, selectable marker genes, replication origins and open reading frames.

Codon Optimization Tool

Find rare codons or produce a fully optimized sequence based on a target organism and remove unwanted restriction sites at the same time.

Simulate cloning operations in one-step

In a few clicks you can

  • Ligate multiple fragments together that have matching overhangs.
  • Insert a fragment of DNA into a vector with matching overhangs
  • Simulate restriction cloning
  • Simulate conventional PCR
  • Simulate InFusion Cloning and Gibson Assembly
  • Simulate TOPO cloning

Store and access important restriction enzyme and DNA fragment data

Drag and drop your important data, customize your restriction enzymes lists and display all of the enzymes on your linear or circular DNA fragment-all in real time. Commercially available enzymes including GoldenGate and BioBrick are already stored in Geneious.

Automatically track and store important documentation

Track Cloning operations so changes can be propagated automatically from parents to all descendants.


Download a free trial and one of our tutorials to get to grips with the functionality of Geneious interactively.

Tutorial- Gibson Assembly

Learn how to simulate Gibson Assembly in Geneious.

Tutorial- Topo Cloning

Learn how to simulate Topo cloning in Geneious, using TA, Blunt or Directional methods.

Tutorial – Restriction Cloning

This tutorial shows you how to use the restriction cloning tools in Geneious to create a plasmid with a functional GFP fusion protein.

Tutorial – Golden Gate Cloning

Learn how to simulate Golden Gate cloning in Geneious, including how to automatically design oligonucleotide primers for generating the overhangs for assembly of parts.

Application Notes

Homology-Based Cloning Methods

Design experiments using exonuclease-based recombination (3’ or 5’ exonuclease) or using homologous recombination.

Geneious has done a great deal for our lab, and I think it adds incredible value for labs with a mixture of wet and dry folks or those doing lots of cloning like ours.  
Cole TrapnellHarvard University