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CodonW

Details

CodonW is a unique program that has been designed to simplify the Multivariate analysis (correspondence analysis) of codon and amino acid usage.
This program also calculates the standard indices of codon usage.
It has both a menu and a command-line interface.
Features:
-Written in ANSI compliant C
-Menu driven
-Extensive number of command line options
-Genetic code independent
-No limits on the number of sequences, the sequence length
-Calculates the codon usage indices:
CAI: Codon adaptation index
Fop: Frequency of optimal codons
Nc: Effective number of codons
CBI: Codon Bias Index
-Calculates amino acid indices
GRAVY score
Aromaticity
-Calculates correspondence analysis of
Codon Usage
RSCU (Relative synonymous codon usage)
Amino acid usage
-Correspondence analysis
can include/exclude codons/amino acids
can generate detailed reports of trends
attempts to identify optimal codons automatically
can allow additional data sets to be added
records any number of trends
-Calculates gene parameters
Gene length
GC, GC3s and codon position specific G+C
Dinucleotide composition (in all three codon frames)
Amino acid usage
Relative amino acid usage
Codon usage
Relative Synonymous codon usage
-Can conceptually translates sequence to protein
-Reformats sequence data
-Human or machine readable output
-Can concatenate genes (whilst preserving reading frame) to calculate
overall codon usage
GC content
Dinucleotide composition
-Generates tables of codon, amino acid, or RSCU usage
-Can even help you learn the Genetic code.
-and more
- 8 out of 10

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