Our Mission: Intuitive Tools for DNA Sequence Assembly and Analysis

CodonCode Corporation provides user-friendly, affordable, and powerful software for DNA sequence assembly, alignment, and analysis.

Our software helps to minimize the time needed to analyze DNA sequencing data through better algorithms and intuitive tools. Many of the unique features in our software were added in direct response to customer suggestions. We back our software with expert support that is based on extensive experience in large-scale DNA sequencing, technology development and evaluation, and bioinformatics.

Milestones

• December 2024:
  CodonCode releases CodonCode Aligner version 12.0. CodonCode Aligner version 12.0 adds three new virtual cloning methods (blunt-end, TOPO and TA cloning), the option to transfer features between sequences, and viewing features in the contig overview for aligned sequences.
   
• July 2023:
  CodonCode releases CodonCode Aligner version 11.0. CodonCode Aligner version 11.0 introduces Gibson Assembly, finding and annotating common features, and synchronizing starts.
   
• December 2021:
  CodonCode releases CodonCode Aligner version 10.0. CodonCode Aligner version 10.0 introduces restriction cloning, sequence maps, and separating alleles.
   
• October 2019:
  CodonCode releases CodonCode Aligner version 9.0. CodonCode Aligner version 9.0 introduces an improved base view, support for EMBL and Genbank features, and new sequence selection tools.
   
• March 2018:
  CodonCode releases CodonCode Aligner version 8.0. CodonCode Aligner version 8.0 introduces support for clustering and identifying sequences for metagenomics; dotplot comparisons; translation-based alignments with MACSE; new menu items to align with Clustal or Muscle; and a new "Import subset" option to filter based on sequences or names.
   
• July 2017:
  CodonCode releases CodonCode Aligner version 7.1. CodonCode Aligner version 7.1 introduces support for NGS data trimming and adapter removal with Bbduk2, and NGS assembly with Tadpole.
   
• February 2017:
  CodonCode releases CodonCode Aligner version 7.0. New features in Aligner 7.0 are RFLP analysis and improved NGS assembly.
   
• October 2015:
  CodonCode releases CodonCode Aligner version 6.0. New features in Aligner 6.0 are primer design and bacterial genome assembly.
   
• November 2014:
  CodonCode releases CodonCode Aligner version 5.1. Aligner 5.1.1 introduces Methylation Analysis and Virtual Gels.
   
• March 2014:
  CodonCode releases CodonCode Aligner version 5.0. New features in this version include alignments with Bowtie2 and Clustal Omega, displaying paired ends for Bowtie2 alignments, improved gap movement edits, contig overview printing, and multiple speed and memory improvements for large projects and alignments. Aligner 5.0 is comatible with Windows 8 and OS X Mavericks (10.9).
   
• June 2013:
  CodonCode releases CodonCode Aligner version 4.2. Aligner 4.2 introduces support for 64-bit Windows. On 64-bit versions of Windows, CodonCode Aligner 4.2 can now use memory beyond the 1.4 GB limit on 32-bit Windows, up to the available amount of physical memory (RAM).
   
• March 2013:
  CodonCode releases CodonCode Aligner version 4.1. New features in this version include additional filters for the difference table and the option to switch between a stacked and packed overview for aligned samples. Aligner 4.1 is comatible with Windows 8 and OS X Mountain Lion (10.8).
   
• May 2012:
  CodonCode releases CodonCode Aligner version 4.0. New features in this version include better support for large projects, support for FASTQ and SAM files, an improved, zoomable contig overview with coverage map, the ability to build trees for selection, split contigs by tree, and a new function to import subsets of samples.
   
• September 2010:
  CodonCode releases CodonCode Aligner version 3.7. New features in this version include replacing gaps in the consensus and making features upper and lower case.
   
• December 2009:
  CodonCode releases CodonCode Aligner version 3.5. New features in this version include Neighbor-Joining trees, zooming in the contig view, new consensus methods, and faster assemblies and alignments.
   
• March 2009:
  CodonCode releases CodonCode Aligner version 3.0. New features in this version include options to see translations for all samples, translation-based background colors, scripting and speed improvements, and better handling of larger projects.
   
• September 2007:
  CodonCode releases CodonCode Aligner version 2.0. New features in this version include restriction maps, print previews, customizable toolbars, support for scripting, and alignment to reference sequences based on sample names.
   
• November 2006:
  CodonCode releases CodonCode Aligner version 1.6. Among other new features, this version introduces support for the Aligner License Server, which allows the sharing of licenses between any number computers, including mixes of Windows and OS X computers.
   
• January 2006:
  CodonCode releases CodonCode Aligner version 1.5. This version introduces the option to align contigs to each other, while maintaining the link to the sequence traces that were used to generate the contigs.
   
• March 2004:
  CodonCode releases CodonCode Aligner version 1.2.0. New in this version is the ability to identify heterozygous point mutations in aligned sequences. Together with the ability to identify and analyze heterozygous insertions and deletions, CodonCode Aligner now offers a complete set of tools for mutation analysis.
   
• June 2003:
  CodonCode releases CodonCode Aligner, a Phred-Phrap compatible assembler and contig editor for Windows and Mac OS X.
   
• September 1999:
  CodonCode releases TraceViewer, a Java program to view sequence traces and Phred quality scores.
   
• March 1999:
  CodonCode Corp. obtains distribution licenses for Consed, the contig editing and finishing program for the Phred-Phrap package.
   
• July 1998:
  CodonCode Corp. completes a major consulting project with a sequencing instrumentation company. Results were presented at the 10th International Genome Sequencing and Analysis Conference in Miami Beach, Florida, September 1998, and are available as an on-line poster.
   
• June 1998:
  CodonCode Corp. obtains distribution licenses for Phred, Phrap, Cross_match, and Swat, a leading software package developed by Dr. Phil Green and co-workers at the University of Washington. Cross_match, and Swat, a leading software package developed by Dr. Phil Green and co-workers at the University of Washington.
  
   

Publications

CodonCode Aligner has been used and cited in thousands scientific publications by researchers all over the world. Here is a list of publications that cite CodonCode Aligner.

Relevant publications and abstracts by CodonCode employees:

• Li-Cor Generated Trace Files: Optimization Of Processing Parameters For Phred And Phrap, And Comparison To Sequences Generated On Four-Color Sequencers
  Peter Richterich, Pat Humphrey & Jim Amen (1998), Poster at the 10th International Genome Sequencing and Analysis Conference, Miami Beach, Florida, September 1998
  
• Estimation of errors in "raw" DNA sequences: A validation study
  Peter Richterich (1998), Genome Research 8: 251-259
• Multiplex sequencing of 1.5 Mb of the Mycobacterium leprae genome
  Douglas R. Smith, Peter Richterich, Marc Rubenfield, et al. (1997), Genome Research 7: 802-819