# Virus-Host Codon Usage Co-Adaptation Analysis

## Documentation for package ‘vhcub’ version 1.0.0

- DESCRIPTION file.

## Help Pages

vhcub-package | vhcub: A package to analysis the co-adaptation of codon usage between a virus and its host.
CAI.values | Codon Adaptation Index (CAI)
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).
ENc.GC3plot | ENc-GC3 scatterplot.
ENc.values | Effective Number of Codons (ENc).
fasta.read | Read fasta formate and convert it to data frame
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)
vhcub | vhcub: A package to analysis the co-adaptation of codon usage between a virus and its host.