CodonCode Aligner is user-friendly software for DNA sequence assembly and alignment. Features include end clipping, vector trimming, sequence assembly, alignment to reference sequences, cDNA to genomic DNA alignment, contig editing, phylogenetic trees, and mutation detection. CodonCode Aligner offers many time saving and unique features, including the ability to align contigs with Clustal and muscle, trace sharpening, and base calling with Phred.

CodonCode Aligner is user-friendly software for DNA sequence assembly, alignment, contig editing, and mutation detection. In addition to features common in sequence assembly programs like end clipping, alignments to reference sequences, and exporting, CodonCode Aligner offers many unique features not found in other software. Advanced CodonCode Aligner features include: - Assemble by name: build hundreds of contigs in seconds, based on sample names - Accurate consensus sequences based on sequence qualities eliminate the need to edit trivial discrepancies - Contigs of contigs: align contigs to each other with ClustalW, and go back to the underlying traces with a simple double-click - Automate with one-step processing and scripts - Sensitive mutation analysis with unique tools for analyzing heterozygous insertions and deletions - Use leading tools like Clustal, MUSCLE, Phred & Phrap within CodonCode Aligner - Get a better look at your ABI sequences with CodonCode Alignerapos;s trace sharpening - Look at differences with the difference table and zooming in contigs - Build Neighbor-Joining trees to sort your samples by differences CodonCode Aligner is easy to learn and use, yet powerful and highly customizable. It includes extensive, context-sensitive help with "how to" instructions and explanations about the algorithms used. CodonCode Aligner is widely used in phylogenetics, evolution research, biogeography, mutation detection, and other biomedical research areas. The download is a trial version that is fully functional for 30 days. It can be converted into a full version by purchasing a license. Licenses for CodonCode Aligner are substantially less expensive than licenses for comparable software packages. "Floating" licenses are available at no additional cost, and can be shared between Windows and Mac OS X.

Major Update
New: Neighbor-Joining trees
Zooming in alignments & assemblies
Automatic reference sequence shortening after alignments
Mask low coverage regions
New and flexible consensus methods
Set base numbers
Automatic name scheme definitions for quot;Assemble & Align by Namequot;
Customize toolbars directly through popup menus
Rebuild the consensus
See http://www.codoncode.com/aligner/new.htm
[ CodonCode Aligner Sequence Assembler release history ]

Windows 2000 or newer, Mac OS X 10.4 or newer

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