Provided by: codonw_1.4.4-2_amd64 bug


       codonw - Correspondence Analysis of Codon Usage


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

              This help message

              Prevent the menu interface being displayed

              Prevent warnings about sequences being displayed

              Overwrite files silently

              Concatenate all genes in inputfile

              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

              Base composition at synonymous third codon positions

       -L_sym Number of synonymous codons

       -L_aa  Total number of synonymous and non-synonymous codons

              All the above indices

       -aro   Calculate aromaticity of protein

       -hyd   Calculate hydropathicity of protein

              {file}      User input file of CAI values

              {file}      User input file of CBI values

              {file}      User input file of Fop values

       Correspondence analysis (COA) options

              COA of codon usage frequencies

              COA of Relative Synonymous Codon Usage

              COA of amino acid usage frequencies

              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 format (codons are separated by spaces)

              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 <>