News

  • September 20, 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 2, 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 30, 2006:
    CodonCode releases CodonCode Alignerversion 1.5. One of the many new features is the ability to compare (align) contigs, while keeping the connection to underlying traces. This feature was requested by many users who work on evolution or population genetics projects.
      
  • June 10, 2005:
    CodonCode releases CodonCode Aligner version 1.4.1. This version offers a <>number of improvements that were requested by our users, including improved gap placement in assemblies and alignments, the ability to create folders to organize unassembled sequences, and a number of improvements for mutation detection.
      
  • 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.
     
  • January 2004:
    CodonCode releases CodonCode Aligner version 1.1.5. New in this version is the ability to identify and analyze heterozygous insertions and deletions.
     
  • June 2003:
    CodonCode Corporation released CodonCode Aligner, a Phred-Phrap compatible contig editor and assembler for Windows and Mac OS X. CodonCode Aligner offers access to modern algorithm with a familiar, easy-to-learn user interface.
         
  • A new version of CodonCode's TraceViewer was released on December 5, 2001. It provides a quality overview window for individual sequence traces, better printing support, and OS X compatibility.
     

 

Publications

Recent 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

Other publications relevant to products and services CodonCode Corporation is offering:

  • "Base calling of automated sequencer traces using PHRED. I. Accuracy assessment."
    Brent Ewing, LaDeana Hillier, Michael C. Wendl & Phil Green (1998), Genome Research 8: 175-185
  • "Base calling of automated sequencer traces using PHRED. II. Error Probabilities."
    Brent Ewing & Phil Green (1998), Genome Research 8: 186-194
  • "Automating the identification of DNA variations using quality-based fluorescence resequencing: analysis of the human mitochondrial genome"
    Mark J. Rieder, Scott L. Taylor, Vincent O. Tobe & Deborah A. Nickerson (1998), Nucleic Acids Research 26: 967-973

 

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