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        CodonW was 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.

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        Readme.Links

        CodonW can emulate a range of useful utility codon usage and sequence analysis programs. These programs perform tasks that CodonW can also accomplish, but where often several menu items or commandline options need to be selected. Making several menu selections every time you want to concepually translate sequences into protein is tedious; likewise maintenance of these auxiliary programs can often be time-consuming. Therefore, when designing codonW I tried to minimise these problems. When the first program argument (i.e. the name which you call the executable program) matches a list of accepted names, the executable file (i.e. codonW) will emulate the program appropriately.

        For example, if we start codonw using its normal name 

        ./codonw					(starts menu interface)
Welcome to CodonW  1.3  for Help type h
  Initial Menu 
  Options
         (1) Load sequence file
         ( )
         (3) Change defaults
         (4) Codon usage indices
         (5) Correspondence analysis
         ( )
         (7) A bit of fun
         (8) Change the output written to file
         (9) About C-codons
         (R) Run C-codons
         (Q) Quit

        we see the menu interface, however if we rename codonw to transl (one of the recognised list of names) then we see a much more succinct interface.

        

mv codonw transl            (mv is UNIX for rename)
./transl                    (translates DNA to AA)

DNA 2 AA translating Program

Name of input filename (h for help) [input.dat]

        Though the commandline is largely unnecessary when emulating these auxiliary programs, it is still functional. Commandline options such as concatenating genes, selecting machine or human readable output, or selecting an alternative genetic code are still valid.

        The accepted program names and the functions/tasks that are emulated are

        Name

        Function

        cu

        Counts codon usage

        cutab

        Counts and tabulates codon usage

        cutot

        Counts and tabulate total codon usage of all genes

        rscu

        Calculate relative synonymous codon usage

        aau

        Count amino acid usage

        raau

        Calculate relative amino acid usage

        tidy

        Reformat sequences into fasta/Pearson format

        reader

        Reformat input sequence data into space codons

        transl

        Reformat DNA by conceptually translating to protein

        bases

        Calculates base composition in each reading frame

        gc3s

        Calculates GC content of synonymous third codon positions

        gc

        Calculates GC content of each gene

        base3s

        Calculate base composition of synonymous third codon positions

        dinuc

        Calculates dinucleotide frequency in three frames

        cai

        Calculates codon adaptation index

        fop

        Calculates frequency of optimal codons

        enc

        Calculates effective number of codons

        cbi

        Calculates codon bias index

         

        All the above programs are created during the default codonw build process (i.e. codonWinstall all).

        For the most up to date version and contact information see http://codonw.sourceforge.net/ReadmeLinks.html