Sequence Alignment Software for DNA Data

CodonCode Aligner is advanced yet intuitive sequence alignment software developed to meet the needs of scientists working with DNA sequencing data. From individual reads to large-scale projects, Aligner streamlines the alignment process with fast and reliable tools tailored for both beginners and experienced users. Built-in support for automatic sequence alignment saves time by trimming low-quality ends, aligning chromatogram and text files, and detecting sequencing errors - all with minimal user intervention.

For more complex analyses, the software enables accurate pairwise and multiple sequence alignment, allowing users to compare, edit, and annotate sequences in a visual, interactive environment. Whether you're analyzing Sanger sequencing results, preparing data for cloning, or conducting SNP or mutation studies, CodonCode Aligner delivers the precision and flexibility you need. With support for a wide range of input formats, including .ab1, .scf, FASTA, FASTQ, EMBL and GenBank files, Aligner is the ideal solution for efficient, high-quality DNA sequence analysis.

Why Choose CodonCode Aligner for Sequence Alignment?

Multiple Sequence Alignment Made Easy

CodonCode Aligner simplifies the process of multiple sequence alignment, making it accessible for researchers at all experience levels. Whether you are aligning coding regions, comparing different samples, or building a consensus sequence, Aligner delivers fast and accurate results.

Key features include:

• Multiple sequence alignment of DNA sequences from chromatogram or text files
• Align sequences to each other or to a reference sequence
• Automatically detects sequence orientation and reverse complements sequences accordingly
• Integrated base calling and trimming ensure clean input for better results
• Visual display of aligned sequences with color-coded differences and quality indicators
• Manual and automated editing tools let you fine-tune alignments when needed
• Edit and align in the same place without the need for data duplication
• Support for MUSCLE, ClustalW, Bowtie2, translation-based methods, and several built-in alignment algorithms
• Easily generate alignments with different algorithms for your data and compare alignments to find the best result
• Export alignments in commonly used format like NEXUS/PAUP and Phylip.

CodonCode Aligner is ideal for a wide range of workflows - from sequence comparison and cloning to SNP detection and mutation analysis - providing the accuracy you need without the complexity of command-line tools or external alignment packages.

Powerful Alignments to Reference Sequences

Align your sequences to reference sequences you designate. CodonCode Aligner lets you designate multiple reference sequences, and will automatically pick the best reference sequence for each sample.

Use reference sequence alignments to:

• Find differences to known sequences
• cDNA to genomic DNA alignments
• Combine sequences into a contig even if they do not overlap
• Limit your analysis to the region you are interested in

You have full control: Choose whether the reference sequence should be ignored when building the consensus, or used as the consensus sequence. When ignoring the reference sequence, you can pick which character to use in regions without coverage to simplify downstream analysis with BLAST or other tools.

Automatic Sequence Alignment with Preprocessing

CodonCode Aligner saves time and reduces errors with built-in tools for automatic sequence alignment and quality-based trimming. Instead of spending hours manually preparing sequences and checking for errors, Aligner intelligently handles routine steps for you - from trimming poor-quality ends to aligning sequences against a reference.

Automation features include:

• Automatic alignment of multiple chromatogram or FASTA/FASTQ files
• Optional quality trimming of low-confidence bases before alignment
• Automatic detection of vector sequences and poor-quality regions
• Alignments can be performed to reference sequences or between sequences
• Batch processing of large numbers of files with just a few clicks
• For NGS data, trim reads and remove adapter sequences with BBDuk2
• Run Bowtie 2 directly from CodonCode Aligner

Whether you're assembling reads for cloning or comparing sample variants, you stay in control at every step - preview trimming results, inspect alignments, and adjust settings as needed.

Editing and Reviewing Aligned Sequences

CodonCode Aligner has an intuitive interface for reviewing, editing, and validating your results. Whether you want to manually adjust a base, inspect a low-quality region, or explore differences between sequences, Aligner makes the process easy and transparent.

Key features for editing and review include:

• Visual alignment editor with color-coded differences, base quality indicators, and zooming
• Chromatogram trace viewer to verify base calls directly from raw data
• Easy manual editing of alignments, including insertions, deletions, and reordering gaps
• Side-by-side comparison of aligned sequences with highlighting of mismatches
• Consensus sequence generation and annotation tools
• Quick navigation to trimmed ends, vector regions, and gaps, or any other defined regions of interest
• Mask bases that match the consensus, so you can quickly see the bases that are different

With CodonCode Aligner, you don't have to rely solely on automated results - you can easily validate and fine-tune alignments to ensure accuracy for downstream applications like SNP detection, cloning, or submission to sequence databases.

Direct Alignments of Contigs

CodonCode Aligner lets you align sequences to each other with MUSCLE, ClustalW, or the built-in alignment methods. A typical use is to first assemble several sequence reads for each clone into contigs, and then align the consensus sequences for the contigs.

When you want to compare consensus sequences, most other programs force you to either duplicate the consensus sequences, or to export the sequences for alignment with a separate outside program like Clustal. To verify any differences, you then have to work with two separate copies of your sequence data.

CodonCode Aligner can greatly simplify this step:

• Align your contig sequences directly in CodonCode Aligner, while keeping the relation to the underlying sequence traces intact
• Go back to the sequence traces with a simple double-click
• Just one linked copy of your data means you can edit anywhere - in the sequence traces, the consensus sequence, or the alignment of contigs. Updates in the other views will be done automatically
• Choose between the standard multiple sequence alignment programs MUSCLE and ClustalW, or use the built-in algorithms to control parameters like minimum percent identity
• Align samples based on names - automatically create different contigs for different groups of sequences.
• View amino acid translations to see changes that affect the translation.

Supported File Types and Input Options

CodonCode Aligner supports a wide variety of file formats commonly used in DNA sequencing, ensuring easy integration into most research workflows. You can import chromatogram files such as .ab1, .abi, and .scf, as well as text-based formats like FASTA, GenBank, and EMBL. Alignment results can be exported in several different formats too.

Working with your data is simple and efficient. You can drag and drop files directly into the application, or import entire batches of sequences at once. CodonCode Aligner automatically detects file types, recognizes sequence orientation, and can optionally perform trimming and base calling. With support for a wide range of input formats and an intuitive import process, CodonCode Aligner helps you get started with your analysis faster - without the need for manual reformatting or preprocessing.

Applications and Use Cases

CodonCode Aligner is trusted by researchers around the world for a wide range of DNA analysis tasks. Its flexibility and ease of use make it suitable for everything from routine lab work to complex research projects.

Common use cases include:

Sequence and Clone Comparison

Align and verify overlapping reads, check for mutations, and prepare accurate consensus sequences.

Mutation and SNP Detection

Compare sequences to a reference and automatically identify SNPs or insertions/deletions and resulting amino acid changes.

Quality Control and Troubleshooting

Review chromatograms, trim low-quality regions, and identify potential sequencing problems before they affect downstream results.

Sequence Verification

Review base calls, reading frames, or translations to confirm accuracy before downstream analysis or publication.

Primer Walking Projects

Align long sequences generated by successive reads with overlapping primers.

Submission Prep

Clean and annotate sequences for submission to databases such as GenBank.

With tools tailored for both routine workflows and detailed investigations, CodonCode Aligner helps researchers save time, improve accuracy, and streamline their sequence analysis pipeline.

Go Beyond Alignment with Powerful Editing and Assembly Tools

CodonCode Aligner offers more than just alignment - it's a full-featured toolkit for DNA sequence analysis. Easily assemble contigs from overlapping reads, edit base calls and annotations, detect mutations, and prepare high-quality consensus sequences for downstream analysis or submission.

Learn more about:

• Sequence Assembly
  Choose algorithms, including local, global, large gap, and NGS. Assemble Sanger sequences, text sequences, bacterial genomes, and small NGS sequencing projects. Assemble in groups, based on sample names.
• Sequence and Contig Editing
  Automatically remove low-quality regions and vector sequences, and fix sequencing errors with automated tools based on quality and contig sequences.
• Mutation Detection
  Find SNPs and heterozygous mutations, see effects of mutations on translated products, and quickly verify or correct mutation analysis results.
• Molecular Cloning
  Explore virtual molecular cloning methods in CodonCode Aligner. Use alignments to verify your clones.
• Phylogenetic Trees
  Generate phylogenetic trees for your alignments and assemblies.
• Compare Differences
  See color-coded difference tables to quickly find and naviagte to differences between your aligned sequences.

Whether you are assembling genes, verifying clones, or cleaning up sequences for GenBank, CodonCode Aligner gives you the tools to do it all - quickly and accurately.