This is the command codonw that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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 <>
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