CodonCode Aligner - DNA Sequence Assembly and Alignment on Windows and Mac OS X

CodonCode Aligner is a program for sequence assembly, contig editing, and mutation detection, available for Windows and Mac OS X. 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 shots:

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With CodonCode Aligner, you can:

Import sequences from text files	Import sequences from ABI, SCF, and FASTQ files
End clip	Vector trim
Assemble contigs	Align to a reference sequence
Align contigs to each other while keeping links to the traces	Assemble or align in groups, based on sample names
Find heterozygous mutations	Analyze heterozygous insertions and deletions
Design primers	Quickly navigate between user-defined features
Generate phylogenetic trees and restriction maps	Run Phred and Phrap directly from Aligner projects
Export sequences and features	See difference tables and protein translations
Find enzymes for RFLP analysis & create virtual gels	Analyze methylated sequences & view raw trace data
Pland and visualize restriction cloning steps	Separate alleles
Define regions of interest ("features"), for example low quality consensus regions	Assemble bacterial genomes and small NGS sequencing projects

CodonCode Aligner lets you take full advantage of modern algorithms for base calling and sequence assembly, without forcing you to learn complicated command line options or Perl programming.

Interested? Go ahead and download the demo version of CodonCode Aligner. The demo version is a fully functional trace viewer and editor. First-time users get an automatic 30-day trial that allows you to try the out all functions in CodonCode Aligner.

After downloading, we suggest that you watch the introduction video to familiarize yourself with Aligner's most important features.

We occasionally make discounted licenses available to registered fans of CodonCode Aligner on Facebook - please check CodonCode Aligner on Facebook for details!

CodonCode Aligner on Facebook