.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
.TH CODONW "1" "July 2018" "codonw 1.4.4" "User Commands"
.SH NAME
codonw \- Correspondence Analysis of Codon Usage
.SH DESCRIPTION
codonW [inputfile] [outputfile] [bulkoutfile] [options]
General options and defaults:
.TP
\fB\-h\fR(elp)
This help message
.TP
\fB\-nomenu\fR
Prevent the menu interface being displayed
.TP
\fB\-nowarn\fR
Prevent warnings about sequences being displayed
.TP
\fB\-silent\fR
Overwrite files silently
.TP
\fB\-totals\fR
Concatenate all genes in inputfile
.TP
\fB\-machine\fR
Machine readable output
.TP
\fB\-human\fR
Human readable output
.TP
\fB\-code\fR N
Genetic code as defined under menu 3 option 5
.TP
\fB\-f_type\fR N
Fop/CBI codons as defined by menu 3 option 6
.TP
\fB\-c_type\fR N
Cai fitness values as defined by menu 3 option 7
.TP
\fB\-t\fR (char)
Column separator to be used in output files (comma,tab,space)
.PP
Codon usage indices and Amino acid indices
.TP
\fB\-cai\fR
calculate Codon Adaptation Index (CAI)
.TP
\fB\-fop\fR
calculate Frequency of OPtimal codons index (FOP)
.TP
\fB\-cbi\fR
calculate Codon Bias Index (CBI)
.TP
\fB\-enc\fR
Effective Number of Codons (ENc)
.TP
\fB\-gc\fR
G+C content of gene (all 3 codon positions)
.TP
\fB\-gcs3\fR
GC of synonymous codons 3rd positions
.TP
\fB\-sil_base\fR
Base composition at synonymous third codon positions
.TP
\fB\-L_sym\fR
Number of synonymous codons
.TP
\fB\-L_aa\fR
Total number of synonymous and non\-synonymous codons
.TP
\fB\-all_indices\fR
All the above indices
.TP
\fB\-aro\fR
Calculate aromaticity of protein
.TP
\fB\-hyd\fR
Calculate hydropathicity of protein
.TP
\fB\-cai_file\fR
{file}      User input file of CAI values
.TP
\fB\-cbi_file\fR
{file}      User input file of CBI values
.TP
\fB\-fop_file\fR
{file}      User input file of Fop values
.PP
Correspondence analysis (COA) options
.TP
\fB\-coa_cu\fR
COA of codon usage frequencies
.TP
\fB\-coa_rscu\fR
COA of Relative Synonymous Codon Usage
.TP
\fB\-coa_aa\fR
COA of amino acid usage frequencies
.TP
\fB\-coa_expert\fR
Generate detailed(expert) statistics on COA
.TP
\fB\-coa_axes\fR N
Select number of axis to record
.TP
\fB\-coa_num\fR N
Select number of genes to use to identify optimal codons
values can be whole numbers or a percentage (5 or 10%)
.PP
Bulk output options | only one can be selected per analysis
.TP
\fB\-aau\fR
Amino Acid Usage (AAU)
.TP
\fB\-raau\fR
Relative Amino Acid Usage (RAAU)
.TP
\fB\-cu\fR
Codon Usage (CU) (default)
.TP
\fB\-cutab\fR
Tabulation of codon usage
.TP
\fB\-cutot\fR
Tabulation of dataset's codon usage
.TP
\fB\-rscu\fR
Relative Synonymous Codon Usage (RSCU)
.TP
\fB\-fasta\fR
fasta format
.TP
\fB\-tidy\fR
fasta format
.TP
\fB\-reader\fR
Reader format (codons are separated by spaces)
.TP
\fB\-transl\fR
Conceptual translation of DNA to amino acid
.TP
\fB\-base\fR
Detailed report of codon G+C composition
.TP
\fB\-dinuc\fR
Dinucleotide usage of the three codon pos.
.TP
\fB\-noblk\fR
No bulk output to be written to file
.PP
Where {file} represents an input filename, and N an integer value Controlled exit <>