Automatically Document Cloning Workflows

CodonCode Aligner automatically records each step during your cloning simulation. That way every construct comes with a complete cloning history of how it was made, making it easy to share, recreate and modify your workflows.

How to Use the Cloning History in CodonCode Aligner

The cloning history in CodonCode Aligner can be accessed using the History button at the bottom of the base view.
Cloning fragments are color coded, and the history shows enzyme cut sites and base numbers for all vectors and fragments.
Click on primers that were created during the cloning simulation to see a primer dialog. It contains primer details like primer sequence, melting temperature, overlap, and primer picking parameters used. You can also export primers to fasta files or created them as new sequences in your project from there:

Explore Other Cloning Methods and Features in CodonCode Aligner

CodonCode Aligner supports many molecular cloning techniques, each supported by a cloning history. Browse the pages below to learn how Aligner can help you design, simulate, and verify different cloning workflows:

• Clone Verification
  Automatic clone verification: Quickly group your reads by clones, match them to a reference, and verify if the sequences match your expected clone.
• Gibson Assembly
  Seamless DNA assembly without the need for restriction enzymes — ideal for multi-fragment cloning and scarless constructs.
• HiFi Assembly
  A high-fidelity version of Gibson-style cloning that joins DNA fragments with short overlaps while reducing errors and improving efficiency for complex assemblies.
• Restriction Cloning
  Simulate restriction enzyme digests, ligation, and insert orientation with support for hundreds of enzymes.
• TA Cloning
  Learn how to simulate TA cloning and verify insert orientation before going to the bench.
• Blunt-End PCR Cloning
  Plan and test blunt-end ligation of PCR products and vectors, with annotation and map preview features.
• Directional TOPO Cloning
  Learn how to simulate directional TOPO cloning and verify insert orientation before going to the bench.
• Molecular Cloning
  Overview of virtual molecular cloning methods in CodonCode Aligner.
• Primer Design
  Design primers using Primer3. Adjust parameters like primer characteristics and reaction conditions to create PCR, cloning, and sequencing primers that specifically match your workflow.
• Virtual Gels and RFLP Analysis
  Use virtual gels to verify and plan any gels you use in the lab. You can look at restriction maps and virtual gels for single sequences, or even compare multiple sequences (for example your cloning product in both directions) using the RFLP analysis tool in Aligner.