Virtual Molecular Cloning Software
CodonCode Aligner provides powerful tools for virtual molecular cloning, enabling researchers to design, simulate, and optimize cloning strategies with confidence. Whether you're performing Gibson Assembly, TA Cloning, restriction enzyme-based cloning, or other advanced methods, Aligner offers an intuitive interface for planning digests, designing primers, assembling DNA fragments in silico, and annotating features on plasmid maps and vectors. With support for multiple cloning workflows, CodonCode Aligner allows you to plan and test strategies virtually, so that you get it right in the lab.
Visualize and Complete In Silico Cloning in Just a Few Clicks
Step 1: Choose Cloning Method
Step 2: Select Vector and Insert
Step 3: Design Constructs
Step 4: Simulate Cloning
Accurate In Silico Cloning Reduces Lab Errors
- Detect potential issues like incorrect insert orientation, overlap compatibility, or incompatible overhangs — saving time, reagents, and frustration.
- Easily plan complex assemblies with multiple fragments using methods like Gibson Assembly.
- Detect and easily correct frame shifts before entering the lab.
- Verify clones by looking at the reading frame and generating alignments.
Integrated Primer Design and Enzyme Tools
- Choose the best enzymes for your cloning project. Filter enzymes by compatibility with your vector and insert, number of cut sites, overhang types, and more. View cut positions directly on your sequence or plasmid map.
- Store and customize restriction enzyme data. Save lists based on what is available in your lab.
- Design primers tailored for your cloning strategy automatically. Aligner flags potential issues like cut site mismatches.
Visual Cloning Workflow and Plasmid Mapping
- Visualize and simplify your cloning experiment with step-by-step cloning wizards that guide you through your workflow in a streamlined, researcher-friendly interface.
- View sequence and plasmid maps showing annotated features, enzymes, inserts, and orientation. Zoom to the see the bases in the same window.
- Automatically annotate restriction sites, CDS regions, and functional elements for complete visual verification.
Flexible Sequence Editing
- Make direct sequence edits with full undo support.
- Manually edit primers or add spacers with visual confirmation of annealing sequences during your cloning experiment.
- Easily edit sequences, insert mutations, or trim fragments while keeping annotations and enzyme sites updated in real time.
Benefits of Virtual Cloning with CodonCode Aligner
CodonCode Aligner offers a streamlined, virtual workflow for in silico cloning that helps you avoid common lab pitfalls and get accurate results faster. With preloaded common cloning vectors and automated primer design, Aligner gives you the control and precision you need to succeed — before you ever pick up a pipette.
Simulate Ligation
Virtually test ligation between overhangs for PCR products, inserts, and vectors.
Verify Insert Orientation
Ensure inserts are correctly ligated and in-frame before lab work.
Visualize Plasmid Maps
Automatically generate annotated maps of your virtual constructs.
Design Primers
Create and export primers optimized for specific PCR products.
Avoid Cloning Errors
Catch misoriented inserts, frameshifts, and mismatches before the experiment.
Track & Document
Save, export and annotate your constructs for easy documentation and reproducibility.
Virtual Molecular Cloning Methods in CodonCode Aligner
CodonCode Aligner supports a variety of in silico cloning tools making it easier to plan and execute successful experiments with confidence. Visualize plasmid maps, verify sequences, and simulate ligation with ease.
