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codonw - Correspondence Analysis of Codon Usage

CODONW(1) User Commands CODONW(1)

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 <>
February 2016 codonw 1.4.4