CodonW has been hosted at SourceForge since 2005, its project name is codonw and can be accessed via this link


Correspondence Analysis of Codon Usage

CodonW is a programme designed to simplify the Multivariate analysis (correspondence analysis) of codon and amino acid usage. It also calculates standard indices of codon usage. It has both menu and command-line interfaces. It was written by John Peden in the lab of Paul Sharp,  Dept of Genetics, University of Nottingham. John is working in human genetics and is currently employed as ProCardis database manager at the WTCHG in Oxford University

CodonW was written as part of my PhD thesis on Codon Usage and if you are interested in reading in more depth around codon usage a copy of my thesis can be downloaded from here (1.72Mb).

NB: I have extensively tested it and believe it to be bug free. If you find a bug or something confusing please email me and let me know (Don't forget to tell me the Operating System and to send me the input file that generated the error).

Downloading and Installation

Binaries are available for the following operating systems.

1.Compaq Tru64

2. Irix 6.5 (64 bit)

3. Solaris 2.6(solaris)

4. Win 32bit (NT/95/98/2000/XP) (No GUI; runs within a DOS emulation window)

5. MacOS X version, (No GUI and runs from MacOS Unix terminal/commandline)

6. Web access via PISE at the pasteur

Alternatively you can download the source code in zip or gzip format and compile it yourself. See the README file for more information.


  1. Written in ANSI compliant C
  2. Menu driven
  3. Extensive number of command line options
  4. Genetic code independent 
  5. No limits on 
    1. number of sequences 
    2. sequence length
  6. Calculates the codon usage indices


    1. CAI: Codon adaptation index
    2. Fop: Frequency of optimal codons
    3. Nc: Effective number of codons
    4. CBI: Codon Bias Index 
  1. Calculates amino acid indices


    1. GRAVY score
    2. Aromaticity
  1. Calculates correspondence analysis of 
    1. Codon Usage
    2. RSCU (Relative synonymous codon usage)
    3. Amino acid usage
  2. Correspondence analysis 
    1. can include/exclude codons/amino acids
    2. can generate detailed reports of trends
    3. attempts to identify optimal codons automatically
    4. can allow additional data sets to be added 
    5. records any number of trends
  3. Calculates gene parameters


    1. Gene length
    2. GC, GC3s and codon position specific G+C 
    3. Dinucleotide composition (in all three codon frames)
    4. Amino acid usage
    5. Relative amino acid usage
    6. Codon usage
    7. Relative Synonymous codon usage
  1. Can conceptually translates sequences to protein
  2. Reformats sequence data
  3. Human or machine readable output
  4. Can concatenate genes (whilst preserving reading frame) to calculate


    1. overall codon usage
    2. GC content
    3. Dinucleotide composition 
  1. Generates tables of codon, amino acid, or RSCU usage
  2. Can even help you learn the Genetic code.
  3. and more

For more information about codonW and codon usage analysis click here or read the documentation that comes with codonw. 

Page maintained by John Peden ( Replace the # with _), last updated 15/Apr/2005