Mutations can be introduced using PCR amplification with primers containing the mutations. This can be mimicked in the software:
- Introduce mutations manually in the sequences before running Homology Based Cloning. Place primers over mutated sites to ensure the mutations are included in the primer sequence.
- Run Homology Based Cloning using the original sequences, and then introduce mutations into the assembled vector. Re-run Homology Based Cloning using the vector containing the mutations.