NAME

       codonw - Correspondence Analysis of Codon Usage

SYNOPSIS

       codonw [inputfile] [outputfile] [bulkoutfile] [options]

DESCRIPTION

       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.

OPTIONS

       -h     Show help message

       -nomenu
              Prevent the menu interface being displayed

       -nowarn
              Prevent warnings about sequences being displayed

       -silent
              Overwrite files silently

       -totals
              Concatenate all genes in inputfile

       -machine
              Machine readable output

       -human Human readable output

       -code N
              Genetic code as defined under menu 3 option 5

       -f_type N
              Fop/CBI codons as defined by menu 3 option 6

       -c_type N
              Cai fitness values as defined by menu 3 option 7

       -t (char)
              Column separator to be used in output files (comma,tab,space)

       Codon usage indices and Amino acid indices

       -cai   calculate Codon Adaptation Index (CAI)

       -fop   calculate Frequency of OPtimal codons index (FOP)

       -cbi   calculate Codon Bias Index (CBI)

       -enc   Effective Number of Codons (ENc)

       -gc    G+C content of gene (all 3 codon positions)

       -gcs3  GC of synonymous codons 3rd positions

       -sil_base
              Base composition at synonymous third codon positions

       -L_sym Number of synonymous codons

       -L_aa  Total number of synonymous and non-synonymous codons

       -all_indices
              All the above indices

       -aro   Calculate aromaticity of protein

       -hyd   Calculate hydropathicity of protein

       -cai_file
              {file}      User input file of CAI values

       -cbi_file
              {file}      User input file of CBI values

       -fop_file
              {file}      User input file of Fop values

       Correspondence analysis (COA) options

       -coa_cu
              COA of codon usage frequencies

       -coa_rscu
              COA of Relative Synonymous Codon Usage

       -coa_aa
              COA of amino acid usage frequencies

       -coa_expert
              Generate detailed(expert) statistics on COA

       -coa_axes N
              Select number of axis to record

       -coa_num N
              Select number of genes to use to  identify  optimal  codons  values  can  be  whole
              numbers or a percentage (5 or 10%)

       Bulk output options | only one can be selected per analysis

       -aau   Amino Acid Usage (AAU)

       -raau  Relative Amino Acid Usage (RAAU)

       -cu    Codon Usage (CU) (default)

       -cutab Tabulation of codon usage

       -cutot Tabulation of dataset's codon usage

       -rscu  Relative Synonymous Codon Usage (RSCU)

       -fasta fasta format

       -tidy  fasta format

       -reader
              Reader format (codons are separated by spaces)

       -transl
              Conceptual translation of DNA to amino acid

       -base  Detailed report of codon G+C composition

       -dinuc Dinucleotide usage of the three codon pos.

       -noblk No bulk output to be written to file

       Some  of  the  codonw  subtools  can  be  directly  accessed using shortcuts prefixed with
       'codonw-'.

AUTHOR

       This manpage was written by Sascha Steinbiss for the Debian distribution and can  be  used
       for any other usage of the program.

SEE ALSO

       codonw-rscu(1),   codonw-cu(1),   codonw-aau(1),  codonw-fop(1),  codonw-raau(1),  codonw-
       tidy(1), codonw-reader(1),  codonw-cutab(1),  codonw-cutot(1),  codonw-transl(1),  codonw-
       bases(1),  codonw-base3s(1), codonw-dinuc(1), codonw-cai(1), codonw-gc3s(1), codonw-gc(1),
       codonw-cbi(1), codonw-enc(1)