Intuitive and Accurate Sequence Assembly

CodonCode Aligner supports flexible workflows for assembling DNA sequences efficiently — with advanced features not found in other tools. Examples include direct comparison of contigs from different clones and trace sharpening to improve readability in low-quality regions.

Sanger Sequencing: Assemble and Edit with Speed and Precision

Assemble projects ranging from a few reads to thousands of reads quickly and accurately, and with minimal setup. CodonCode Aligner offers a number of unique features to streamline the assembly process, for example the ability to group samples by name for assembly, producing separate contigs for each sample group.
When manual editing is required, CodonCode Aligner makes editing fast and intuitive, with additional automated tools to resolve base disagreements, clean up assemblies, and improve overall sequence quality.

Learn more about sequence assembly

Next Generation Sequencing

NGS assembly and scaffolds of a bacterial genome

Assemble bacterial genome and build scaffolds. Align NGS reads to reference sequences with Bowtie 2. Pre-process NGS reads: trim, reformat, and re-pair reads. Cluster and identify sequences. Analyze linkage between alleles in diploid organisms.

Learn more about NGS

Sequence Comparison: Visualize Differences and Align Sequences with Ease

Compare sequences to references or to each other using flexible alignment options and purpose-built tools. CodonCode Aligner presents results in views and tables designed to support interpretation and follow-up analysis.

Fast, Flexible Sequence Alignment and Comparison

Multi sequence alignment with ClustalO showing Sanger sequence trace

Perform pairwise or multiple sequence alignments using integrated tools like Clustal Omega, MUSCLE, Bowtie2, and translation-based methods, or use Aligner’s built-in algorithms for rapid reference-based comparisons.

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Analyze Differences and Mutations

Heterozygous mutation Sanger sequence example

Get a comprehensive view of sequence differences in alignments in customizable difference tables. Tools for mutation detection — including heterozygous base calls and codon-level effects — are available for workflows based on Sanger data.

Learn more about difference tables

Learn more about mutation analysis

Design & Analysis Features for Molecular Biology Applications

CodonCode Aligner includes tools to support molecular biology workflows beyond sequence assembly and alignment. Design primers, simulate restriction digests, plan cloning strategies, and add or review sequence annotations — directly within CodonCode Aligner.

Visualize Restriction Maps and Simulate RFLP Digests

Display restriction maps and visualize cut patterns in virtual gels or tables. Simulate digests for RFLP analysis and compare fragment patterns across samples.

Learn more about restriction mapping

In Vitro Cloning: Fast, Visual Design of Cloning Constructs

Simulate cloning procedures using restriction cloning, Gibson Assembly, TA cloning, and TOPO cloning. Select inserts visually, pick primers automatically, and catch errors before they become problems.

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Design Primers and Annotate Sequences Easily

Design PCR, cloning, or sequencing primers using customizable parameters such as primer length, melting temperature, and product size. Visualize primer locations relative to target regions, review primer characteristics, and export selected primers for ordering.

CodonCode Aligner includes many other tools, such as transferring features between aligned sequences, and finding common plasmid features by identity — check the list of features below for more.

Learn more about primer design

All Features

Discover the many molecular biology and sequence analysis tools available in CodonCode Aligner.

Data Management

Intuitive project structure
Import Sanger sequence chromatograms
Import sequences in common text file formats like Genbank, DNA, and FASTQ
Create new sequences from clipboard contents
Retrieve sequences from Genbank
Export sequences, alignments, translations, features, and differences

Sequence Alignment and Assembly

Assemble Sanger sequences and text sequences
Choose algorithms, including local, global, large gap, and NGS specific
Assemble bacterial genomes and small NGS sequencing projects
Align sequence reads to a reference sequence
Assemble or align in groups, based on sample names
Align contigs to each other while keeping links to the traces

Sequence Editing

Automatically remove low-quality regions and vector sequences
Edit Sanger sequence chromatograms and text sequences
Define regions of interest ("features"), for example low quality consensus regions
Quickly navigate between user-defined features
Remove sequencing errors with automated tools based on quality and contig sequences

Comparing Sequences and Finding Mutations

Create multi sequence alignments with ClustalO, MUSCLE, and CodonCode algorithms
Generate phylogenetic trees and restriction maps
See difference tables and protein translations
Find SNPs and heterozygous mutations
See effect of mutations on translated products
Quickly verify or correct mutation analysis results

Virtual Cloning

Plan in silico cloning experiments using:
- Restriction cloning
- TA cloning and TOPO TA cloning
- Blunt end cloning
- TOPO cloning
- Gibson Assembly
Verify cloning products using assembly, alignment, and difference functions

Analyze and Annotate

Annotate common plasmid elements
Copy feature annotation based on similarity or alignments
Analyze heterozygous insertions and deletions
Find enzymes for RFLP analysis
Create restriction maps and virtual gels
Build phylogenetic trees
Design PCR and sequencing primers

DNA Sequence Alignment, Assembly, and Analysis with CodonCode Aligner