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 <>