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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 <>

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