NAME

       codonw - Correspondence Analysis of Codon Usage

DESCRIPTION

       codonW [inputfile] [outputfile] [bulkoutfile] [options] General options and defaults:

       -h(elp)
              This 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

       Where {file} represents an input filename, and N an integer value Controlled exit <>