CodonCode Aligner

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For short-term use (up to 30 days) in classes, the trial version of CodonCode Aligner may be sufficient, since every student who uses CodonCode Aligner for the first time will automatically get a fully functional 30-day trial after installing CodonCode Aligner. CodonCode Aligner is a leading software program 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. Software similar to or like CodonCode Aligner Commercial application for DNA sequence assembly, sequence alignment, and editing on Mac OS X and Windows. CodonCode Aligner: Paid -DNA Baser: Paid -Free Molecular Cloning Software. Windows: Mac: Linux: SnapGene Viewer: Serial Cloner: UGENE: ApE (A Plasmid Editor) - Decompression Software WinZip Free Online Primer Design Software Primer3 NCBI Primer-BLAST Free Online Oligo Analysis Tools Oligo Calc. Makes CodonCode Aligner a program for sequence assembly, contig editing, and mutation detection. Find out more about CODONCODE CORPORATION, Bioinformatics.

  1. Codoncode Aligner
  2. Codon Codes
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CodonCode Aligner
  • Online teaching with CodonCode Aligner
    by Peter Richterich » Fri Apr 03, 2020 10:09 am
    0 Replies
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    Fri Apr 03, 2020 10:09 am
  • Windows: Using Aligner with high resolution displays
    by Peter Richterich » Fri Jul 15, 2016 2:58 pm
    0 Replies
    12261 Views
    Last post by Peter Richterich
    Fri Jul 15, 2016 2:58 pm
  • Disabling AppNap on OS X
    by Peter Richterich » Thu Apr 09, 2015 9:53 am
    0 Replies
    20682 Views
    Last post by Peter Richterich
    Thu Apr 09, 2015 9:53 am
  • How to get 'extended' keys from the License Server
    by Peter Richterich » Thu Sep 25, 2008 10:13 am
    0 Replies
    20147 Views
    Last post by Peter Richterich
    Thu Sep 25, 2008 10:13 am
  • Using the License Server while traveling
    by Peter Richterich » Thu Sep 25, 2008 9:59 am
    0 Replies
    18698 Views
    Last post by Peter Richterich
    Thu Sep 25, 2008 9:59 am
  • Single-user or Concurrent (License Server) license?
    by Peter Richterich » Wed Sep 03, 2008 10:18 am
    0 Replies
    27088 Views
    Last post by Peter Richterich
    Wed Sep 03, 2008 10:18 am
  • Problems connecting to the Aligner License Server
    by Peter Richterich » Tue Aug 26, 2008 4:53 pm
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    Last post by Peter Richterich
    Tue Aug 26, 2008 4:53 pm
  • How much does a License Server license cost?
    by Peter Richterich » Fri Aug 22, 2008 10:30 am
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    Fri Aug 22, 2008 10:30 am
  • License Issues on macOS 10.14 (Mojave)
    by Peter Richterich » Wed Oct 31, 2018 4:19 pm
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    Last post by Peter Richterich
    Wed Oct 31, 2018 4:19 pm
  • Verify that you are connecting to your own License Server
    by Nina Schweikardt » Mon Feb 20, 2017 4:00 pm
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    Mon Feb 20, 2017 4:00 pm
  • Current license key does not allow you to update
    by Nina Schweikardt » Mon Feb 20, 2017 3:52 pm
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    Last post by Nina Schweikardt
    Mon Feb 20, 2017 3:52 pm
  • Import from Genbank workaround
    by Peter Richterich » Thu Nov 10, 2016 10:48 am
    0 Replies
    12988 Views
    Last post by Peter Richterich
    Thu Nov 10, 2016 10:48 am
  • mutation calling with a reference sequence
    by lno » Tue Nov 24, 2015 11:12 am
    1 Replies
    20362 Views
    Last post by Peter Richterich
    Wed Nov 25, 2015 11:42 am
  • For heterozygosity
    by rayanans » Wed Jan 21, 2015 1:08 pm
    2 Replies
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    Last post by rayanans
    Wed Jan 21, 2015 3:03 pm
  • long gap alignment
    by ssig » Mon Oct 27, 2014 5:16 pm
    1 Replies
    17042 Views
    Last post by Peter Richterich
    Tue Oct 28, 2014 9:15 am
  • Restoring Aligner projects from the Aligner backup file
    by Nina Schweikardt » Tue Jan 28, 2014 1:08 pm
    0 Replies
    18834 Views
    Last post by Nina Schweikardt
    Tue Jan 28, 2014 1:08 pm
  • Source file not found during install
    by Nina Schweikardt » Mon Nov 04, 2013 11:38 am
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    16670 Views
    Last post by Nina Schweikardt
    Mon Nov 04, 2013 11:38 am
  • Aligner_Installer.exe /passive gives problems
    by jasevink » Thu Oct 17, 2013 3:10 am
    2 Replies
    19370 Views
    Last post by Peter Richterich
    Mon Oct 21, 2013 11:02 am
  • Silent Install with MSI for use with License Server
    by nlfdss » Wed Oct 16, 2013 11:03 am
    3 Replies
    22499 Views
    Last post by Nina Schweikardt
    Thu Oct 17, 2013 4:28 pm
  • License Server shows a 'Single-User License'
    by Nina Schweikardt » Thu Aug 22, 2013 10:04 am
    0 Replies
    17457 Views
    Last post by Nina Schweikardt
    Thu Aug 22, 2013 10:04 am
  • Excluding N bases from searches?
    by Nick J » Thu Aug 08, 2013 3:55 pm
    2 Replies
    25771 Views
    Last post by Nick J
    Mon Aug 12, 2013 5:59 am
  • Quality and MID trimming
    by BOM86 » Wed Mar 20, 2013 9:03 am
    1 Replies
    16980 Views
    Last post by Peter Richterich
    Thu Mar 21, 2013 8:52 am
  • Installer problems on Windows
    by Peter Richterich » Mon Mar 04, 2013 12:57 pm
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    18404 Views
    Last post by Peter Richterich
    Mon Mar 04, 2013 12:57 pm
  • Using Ref sequence in 'Assemble in Groups'
    by jt-umdnj » Thu Jan 24, 2013 12:38 pm
    1 Replies
    21554 Views
    Last post by Nina Schweikardt
    Wed Feb 06, 2013 3:47 pm
  • New Project Format in CodonCode Aligner 4.0
    by Nina Schweikardt » Thu Jan 17, 2013 12:25 pm
    0 Replies
    17120 Views
    Last post by Nina Schweikardt
    Thu Jan 17, 2013 12:25 pm

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:

With CodonCode Aligner, you can:

Codoncode Aligner

  • 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 the links to the traces
  • Assemble or align in groups, based on sample names
  • Find heterozygous mutations
  • Analyze heterozygous insertions and deletions
  • Define regions of interest ('features'), for example low quality consensus regions
  • 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
  • Design primers
  • Assemble bacterial genomes and small NGS sequencing projects
  • Find enzymes for RFLP analysis & create virtual gel
  • Analyze methylated sequences & view raw trace data

Codon Codes

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 Vivaldi four seasons fall. 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!