Virus-Host Codon Usage Co-Adaptation Analysis
Codon Adaptation Index (CAI)
Statistical dinucleotide over- and underrepresentation (base model).
Statistical dinucleotide over- and underrepresentation (codon model).
Statistical dinucleotide over- and underrepresentation (syncodon model...
ENc-GC3 scatterplot.
Effective Number of Codons (ENc).
Read fasta formate and convert it to data frame
GC content
Parity rule 2 (PR2) plot
Relative Codon Deoptimization Index (RCDI)
Relative Synonymous Codon Usage (RSCU)
Synonymous codon usage eorderliness (SCUO)
Similarity Index (SiD)
vhcub: A package to analysis the co-adaptation of codon usage between ...
Analyze the co-adaptation of codon usage between a virus and its host, calculate various codon usage bias measurements as: effective number of codons (ENc) Novembre (2002) <doi:10.1093/oxfordjournals.molbev.a004201>, codon adaptation index (CAI) Sharp and Li (1987) <doi:10.1093/nar/15.3.1281>, relative codon deoptimization index (RCDI) Puigbò et al (2010) <doi:10.1186/1756-0500-3-87>, similarity index (SiD) Zhou et al (2013) <doi:10.1371/journal.pone.0077239>, synonymous codon usage orderliness (SCUO) Wan et al (2004) <doi:10.1186/1471-2148-4-19> and, relative synonymous codon usage (RSCU) Sharp et al (1986) <doi:10.1093/nar/14.13.5125>. Also, it provides a statistical dinucleotide over- and underrepresentation with three different models. Implement several methods for visualization of codon usage as ENc.GC3plot() and PR2.plot().