CAI.values              Codon Adaptation Index (CAI)
ENc.GC3plot             ENc-GC3 scatterplot.
ENc.values              Effective Number of Codons (ENc).
GC.content              GC content
PR2.plot                Parity rule 2 (PR2) plot
RCDI.values             Relative Codon Deoptimization Index (RCDI)
RSCU.values             Relative Synonymous Codon Usage (RSCU)
SCUO.values             Synonymous codon usage eorderliness (SCUO)
SiD.value               Similarity Index (SiD)
dinuc.base              Statistical dinucleotide over- and
                        underrepresentation (base model).
dinuc.codon             Statistical dinucleotide over- and
                        underrepresentation (codon model).
dinuc.syncodon          Statistical dinucleotide over- and
                        underrepresentation (syncodon model).
fasta.read              Read fasta formate and convert it to data frame
vhcub                   vhcub: A package to analysis the co-adaptation
                        of codon usage between a virus and its host.
