CodonCode Aligner for Windows 3.0.1

CodonCode Aligner for Windows 3.0.1 is designed as a powerful software for DNA sequence assembly, alignment, contig editing, and mutation detection.

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 Features:

1. Multiple sequence assembly and sequence alignment algorithms
2. Manual and automated sequence editing
3. Align contigs to each other and get back to the underlying trace data with a simple double-click
4. Reference sequences and difference tables
5. Sensitive mutation detection
6. Advanced methods for heterozygous indel analysis
7. Automation tools: assemble by name & scripting
8. Assemble by name: build hundreds of contigs in seconds, based on sample names
   
9. Accurate consensus sequences based on sequence qualities eliminate the need to edit trivial discrepancies
10. Automate with one-step processing and scripts
11. Sensitive mutation analysis with unique tools for analyzing heterozygous insertions and deletions
12. Use leading tools like Clustal, MUSCLE, Phred & Phrap within CodonCode Aligner
13. Get a better look at your ABI sequences with CodonCode Aligners trace sharpening

Enhancements: Version 3 of CodonCode Aligner adds many new features and performance improvements, including:

• View translations for all samples
• Use translation-based background colors
• Difference tables
• Faster assemblies

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