CodonCode Aligner 3.5.5

CodonCode Corporation
34.2 MB
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CodonCode Aligner 3.5.5

CodonCode Aligner – DNA Sequence Assembly and Alignment on Windows and Mac OS X

CodonCode Aligner is a program for sequence assembly, contig editing, and mutation detection, available for Windows and Mac OS X. Aligner is compatible with Phred-Phrap and fully supports sequence quality scores, while offering a familiar, easy-to-learn user interface, as shown in the following screen shot:

With CodonCode Aligner, you can:

  • Import sequences from text files
  • Import sequences from ABI and SCF files
  • End clip
  • Vector trim
  • Assemble contigs
  • Align to a reference sequence
  • Align contigs to each other while keeping the links to the traces
  • Assemble or align in groups, based on sample names
  • Find heterozygous mutations
  • Analyze heterozygous insertions and deletions
  • Define regions of interest ("features"), for example low quality consensus regions
  • Quickly navigate between user-defined features
  • Import and edit Phrap-generated assemblies
  • Run Phred and Phrap directly from Aligner projects
  • Export sequences and features
  • Export Consed-compatible assembly projects

CodonCode Aligner lets you take full advantage of modern algorithms for base calling and sequence assembly, without forcing you to learn complicated command line options or Perl programming.


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