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CodonCode Aligner 5.1.5

An efficient program for DNA Sequence Alignment and Assembly

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CodonCode Aligner screenshotCodonCode Aligner is a powerful utility that was designed for sequence assembly, mutation detection and contig editing tasks. The program is available for both Windows OS and Mac OS X. This application supports sequence quality scores and is compatible with Phred-Phrap, providing an intuitive and easy-to-understand user interface.

You can use CodonCode Aligner for performing various tasks, including import of sequences from text files, ABI files and SCF files. By using this tool, you can also discover heterozygous mutations, assemble contigs, analyze heterozygous deletions and insertions, generate restriction maps and phylogenetic trees, export features and sequences, and many more.

CodonCode Aligner also provides a set of advanced functions, including Vector trim and End clip, which will make your work easier and will increase your productivity. The application also lets you perform a wide range of tasks, such as aligning to a reference sequence, assemble or align in groups (based on sample names), easily navigate between user-defined features, view differences between protein translations and tables, define various regions of interest, etc. You can also run Phred and Phrap directly from your Aligner projects.

This application will help you easily take full advantage of modern algorithms for sequence assembly and base calling, without using complex Perl programming or command line parameters.


  • It's fully compatible with Phred and Phrap.
  • Provides a comprehensive set of features and functions.


  • Special characters in file names may cause problems when importing files.
  • Some shortcuts may not work properly when selecting multiple files.
Name CodonCode Aligner
Version 5.1.5
Developer | see all products from this developer
Product Homepage CodonCode Aligner
License Free to try (Shareware)
Last Week Downloads 1
All Time Downloads 401
Filename Aligner_Installer.exe
Filesize 87.8MB
MD5 Checksum DBFDC1C2DAE37C1BE8A6D9A31F47C628
OS Support Windows All
Category Developer Tools

100% CLEAN Certification

BadgeCodonCode Aligner has been tested by team against viruses, spyware, adware, trojan, backdoors and was found to be 100% clean. Our editors will recheck this software periodically to assure that it remains clean.


Old Versions

Software Date Added
CodonCode Aligner 5.1.5 July 07, 2015 - Latest Version
CodonCode Aligner 5.1.3 December 03, 2014

Download the free CodonCode Aligner