CodonCode Aligner 4.1

CodonCode Aligner is a program for sequence assembly, 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, 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.