CodonWwas written by John Peden in the laboratory of Paul Sharp at the University of Nottingham. It is distributed under the terms of the GNU public license, see the file License included with the distribution. 

CodonW is a package for codon usage analysis. It was designed to simplify Multivariate Analysis (MVA) of codon usage. The MVA method employed in CodonW is correspondence analysis (COA) (the most popular MVA method for codon usage analysis). CodonW can generate a COA for codon usage, relative synonymous codon usage or amino acid usage. Additional analyses of codon usage include investigation of optimal codons, codon and dinucleotide bias, and/or base composition. CodonW analyses sequences encoded by genetic codes other than the universal code. 

Why call it codonW?  

Well, "clustal" (a very popular multiple alignment program by Des Higgins) was originally written in Paul's lab in Trinity College Dublin. Clustal has since been rewritten from FORTRAN into C and undergone several name changes clustal-> clustalv-> clustalw -> clustalx. There was also a program called "codons" written in FORTRAN by Andrew Lloyd (another post-doc in Paul's lab), this was the original inspiration for codonW. An early version of codonW, written in C, was called codonv. When the code was enhanced to include multivariate analysis, what better name than codonW 

CodonW version 1.4.2 May 2005

The source code for CodonW can be obtained from SourceForge . Binaries for a number of platforms are also available at this site. 

To Install and Build on UNIX Platforms

uncompress codonW.tar.Z  
tar -xvf codonW.tar   
cd codonw  
./codonWinstall all (asks some questions, then builds codonw)  

This will ask a few questions regarding 'make' and 'cc' and then configure the installation and compile the programs. If you don't understand the questions, just accept the default by pressing the return key and the installation should be OK using the defaults. The install script by default also creates a number of links to the compiled executable codonW. These links allow codonW to emulate other useful codon usage analysis and sequence manipulation software by passing the menu interface (for more information see README.links). Alternatively you can just elect to only build the main program, and not install the linked programs.

./codonWinstall codonw (compile only)
Once you have successfully built codonw, try these commands to get you started.

./codonw -help (for commandline summary)
./codonw (menu interface)

 There is also a short tutorial available.For the most recent documentation on codonW see http://codonw.sourceforge.net/

To Set the Codonw Help Environment: 

CodonW has an in-built help system, the help file is called codonW.hlp and should be located in the same directory as the executable codonw. Alternatively the help file can be pointed to by the environment variable CODONW_H, if you are using a C shell you can add something similar to this to your .login script.  

setenv CODONW_H file_path 

Where file_path is the fully defined path name for codonW.hlp.  

Additional Files 

Readme.coa- explanation about the output files from the correspondence analysis.  

Readme.links- explanation about the auxiliary programmes created during the making of codonw. 

Tutorial - A quick tutorial on the analysis of codon usage of the open reading frames from Saccharomyces cerevisiae chromosome III.

input.dat - An input file containing 111 open reading frames from Saccharomyces cerevisiae chromosome III. (see Tutorial).

Recoding - A quick explanation about how amino acids and codons have are represented internally within codonW.    

Bugs

Updates

If you have any questions or comments, can contact me via SourceForge or Email