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:

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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.

Interested? Go ahead and download the demo version of CodonCode Aligner. The demo version is a fully functional trace viewer and editor. First-time users get an automatic 30-day trial that allows you to try the out all functions in CodonCode Aligner.

After downloading, we suggest that you take the quick tour to familiarize yourself with Aligner's most important features.