codonw(1) 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 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

calculate Codon Adaptation Index (CAI)
calculate Frequency of OPtimal codons index (FOP)
calculate Codon Bias Index (CBI)
Effective Number of Codons (ENc)
G+C content of gene (all 3 codon positions)
GC of synonymous codons 3rd positions
Base composition at synonymous third codon positions
Number of synonymous codons
Total number of synonymous and non-synonymous codons
All the above indices
Calculate aromaticity of protein
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

Amino Acid Usage (AAU)
Relative Amino Acid Usage (RAAU)
Codon Usage (CU) (default)
Tabulation of codon usage
Tabulation of dataset's codon usage
Relative Synonymous Codon Usage (RSCU)
fasta format
fasta format
Reader format (codons are separated by spaces)
Conceptual translation of DNA to amino acid
Detailed report of codon G+C composition
Dinucleotide usage of the three codon pos.
No bulk output to be written to file

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