CodonW has been hosted at SourceForge since 2005, its project name is codow and can be accessed via this link
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 PlatformsGet the source code from SourceForge
Change directory to the directory where you intend to install 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)
./codonw -help (for commandline summary)
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 FilesIndices - explanation about the various codon usage indices that codonW calculates.
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.
Recoding - A quick explanation about how amino acids and codons have are represented internally within codonW.
BugsIf you do find or notice anything strange please e-mail bug reports/complaints/suggestions please Email. Remember to include an example of the input file (and output files) and the options selected that generated the error, don't forget to tell me the make of computer and operating system it was running under.
UpdatesIf you are interested in hearing about updates, just send me an email and I'll stick you on a mailing list