This software offers user-friendly tools for DNA sequence assembly and alignment, including end clipping, contig editing, and mutation detection. It also facilitates alignment to reference sequences and includes features like difference tables and base calling with Phred.
CodonCode Aligner is a user-friendly software designed for DNA sequence assembly, contig editing, mutation detection, and alignment. It offers many unique features that make it stand out from other sequence assembly programs. One of its advanced features includes Assemble by name, which can build hundreds of contigs in seconds based on sample names. This can be particularly useful for large datasets. CodonCode Aligner also has an accurate consensus sequence-based on sequence qualities, which eliminates the need to edit trivial discrepancies.
Moreover, CodonCode Aligner enables the alignment of contigs to each other using ClustalW, with a simple double-click helping users go back to the underlying traces. The software can be automated with one-step processing and scripts, meaning that users can save time and reduce their workload.
CodonCode Aligner also offers sensitive mutation analysis with unique tools for analyzing heterozygous insertions and deletions. Users can use leading tools like Clustal, MUSCLE, Phred & Phrap within CodonCode Aligner. Additionally, CodonCode Aligner's trace sharpening provides a better look at ABI sequences.
Users can easily spot differences with the difference table and zooming in contigs feature. To sort samples by differences, CodonCode Aligner enables the build of Neighbor-Joining trees.
CodonCode Aligner is not only easy to learn but also highly customizable. It includes extensive, context-sensitive help with "how-to" instructions, and explanations of the algorithms used to aid users. The software is widely used in phylogenetics, evolution research, biogeography, mutation detection, and other biomedical research areas.
Users can download a trial version of CodonCode Aligner, which is fully functional for 30 days before purchasing a license. CodonCode Aligner licenses are much cheaper than licenses for comparable software packages. Lastly, floating licenses are available at no additional cost and can be shared between Windows and Mac OS X.
Moreover, CodonCode Aligner enables the alignment of contigs to each other using ClustalW, with a simple double-click helping users go back to the underlying traces. The software can be automated with one-step processing and scripts, meaning that users can save time and reduce their workload.
CodonCode Aligner also offers sensitive mutation analysis with unique tools for analyzing heterozygous insertions and deletions. Users can use leading tools like Clustal, MUSCLE, Phred & Phrap within CodonCode Aligner. Additionally, CodonCode Aligner's trace sharpening provides a better look at ABI sequences.
Users can easily spot differences with the difference table and zooming in contigs feature. To sort samples by differences, CodonCode Aligner enables the build of Neighbor-Joining trees.
CodonCode Aligner is not only easy to learn but also highly customizable. It includes extensive, context-sensitive help with "how-to" instructions, and explanations of the algorithms used to aid users. The software is widely used in phylogenetics, evolution research, biogeography, mutation detection, and other biomedical research areas.
Users can download a trial version of CodonCode Aligner, which is fully functional for 30 days before purchasing a license. CodonCode Aligner licenses are much cheaper than licenses for comparable software packages. Lastly, floating licenses are available at no additional cost and can be shared between Windows and Mac OS X.
What's New
Version 3.7.1:
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 "Assemble & Align by Name"
Customize toolbars directly through popup menus
Rebuild the consensus
See http://www.codoncode.com/aligner/new.htm