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From CodonCode Corporation:
CodonCode Aligner is user-friendly software for DNA sequence assembly, alignment, contig editing, and mutation detection. Aligner is compatible with Phred-Phrap and fully supports sequence quality scores, while offering a familiar, easy to learn user interface. Features include import sequences from text files, align contigs to each other while keeping the links to the traces, find heterozygous mutations, define regions of interest ("features"), import and edit Phrap-generated assemblies, export sequences and features, import sequences from ABI and SCF files, vector trim, align to a reference sequence, analyze heterozygous insertions and deletions, navigate between user-defined features, and export Consed-compatible assembly projects.
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