Virus-Host Codon Usage Co-Adaptation Analysis

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) , codon adaptation index (CAI) Sharp and Li (1987) , relative codon deoptimization index (RCDI) Puigbò et al (2010) , similarity index (SiD) Zhou et al (2013) , synonymous codon usage orderliness (SCUO) Wan et al (2004) and, relative synonymous codon usage (RSCU) Sharp et al (1986) . 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().