CodonCode Corporation provides leading software programs for Mutation Detection, Trace Viewing, Base Calling, Sequence Assembly, and Contig Editing.
 

Sequence Assembly and Mutation Detection with CodonCode Aligner

CodonCode Aligner is easy-to-use program for sequence assembly, contig editing, and mutation detection. With Aligner, you can:

  • Import sequences from ABI, SCF, and text files
  • View and edit sequence traces
  • Assemble or align to reference sequence
  • Assemble or align in groups by name
  • Align contigs with ClustalW or muscle, and go back to the original traces by double-clicking
  • Find heterozygous point mutations
  • Find and analyze heterozygous insertions and deletions
  • End clip
  • Trim vector sequence
  • Define "regions of interest" like discrepancies, low-quality consensus sequences, or tags, and quickly navigate to these regions
  • Export sequences, assemblies, project summaries, and features

CodonCode Aligner is available for Mac OS X and Windows. Free demo versions are available for download. The demo version of CodonCode Aligner is a fully functional trace viewer and editor. Licenses for academic research are available at a 50% discount; prices for single-user academic licenses start at $960 . Multiple licenses are available at substantial discounts.

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 Aligner contigs, quality view, mutation traces  

Trace Viewing and Editing

CodonCode offers free programs for viewing, editing, and printing sequence traces for a number of different operating systems:

Mutation Detection

CodonCode offers two choices for mutation detection and analysis in DNA sequence traces:

  • CodonCode Aligner can find heterozygous point mutations, and find and analyze heterozygous insertions and deletions. CodonCode Aligner is an interactive program that also offers functions for base calling, trace viewing and editing, sequence assembly, and more.
    CodonCode Aligner is available for Mac OS X and Windows.
  • PolyPhred is a tool to find heterozygous mutations in "batch mode", and is well suited for large-scale mutation analysis projects. PolyPhred also requires Phred for base calling and sequence assembly, and typically is used with a contig editor like Consed or CodonCode Aligner.
    CodonCode Corporation distributes PolyPhred under license from the University of Washingon. Academic users should obtain PolyPhred free of charge directly from the authors.
    PolyPhred is available for UNIX, Linux, and Mac OS X, but not for Windows.

Base Calling

For base calling of DNA sequence traces, CodonCode distributes Phred, which many scientists consider as the "gold standard" for base calling. Phred executables are available for Windows, Mac OS X, Linux, and UNIX. Academic users can obtain source code for Phred free of charge directly from the authors.

Phred does not provide a graphical user interface, since Phred is typically run from automated scripts. For users who want to run Phred from a graphical user interface, we suggest CodonCode Aligner. CodonCode Aligner makes it easy to base call with Phred - just select your sequence and choose "Call bases". A workstation version of Phred is included with CodonCode Aligner. This workstation version, which can be used only fromCodonCode Aligner, is free to academic customers.

Sequence Assembly

CodonCode offers two choices for sequence assembly:

  • CodonCode Aligner supports assemblies for up to 2,000 reads from an easy-to-learn user interface. In addition to its build-in assembly algorithm, CodonCode Aligner can also use Phrap to generate assemblies. CodonCode Aligner includes functions for end clipping, vector trimming, contig editing, and more. CodonCode Aligner is available for Mac OS X and Windows.
  • For very large assemblies, CodonCode distributes Phrap under license from the University of Washingon. Like Phred, Phrap does not provide a graphical user interface, since Phrap is typically run from automated scripts. Phrap is available for Mac OS X, Windows, Linux, and UNIX. Typically, Phrap users also need a contig editor like Consed or CodonCode Aligner.
    Academic users can obtain source code for Phrap free of charge directly from the authors.

Contig Editing
 

CodonCode offers two choices for contig editing:

  • CodonCode Aligner allows you to edit assemblies with up to 2,000 reads from an easy-to-learn user interface on Mac OS X and Windows. .
  • For contig editing on UNIX and very large assemblies, CodonCode distributes Consed under license from the University of Washingon. Consed is available for Mac OS X, Linux, and UNIX. Consed is not available for Windows.
    Academic users can obtain Consed free of charge directly from the authors.

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