CodonCode Aligner

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CodonCode Aligner is an 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
  • Find heterozygous point mutations
  • Find and analyze heterozygous insertions and deletions
  • Call bases with Phred
  • 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 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.

The Software allows you to edit assemblies with up to 2,000 reads from an easy-to-learn user interface on Mac OS X and Windows.

One 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.

Addittionaly it can also be used as a fully functional trace viewer and editor.

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