vhcub

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().

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