Virus-Host Codon Usage Co-Adaptation Analysis R package vhcub version 1.0.0 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(). Software Imports: Biostrings, coRdon , ggplot2, seqinr, stringr Suggests: testthat Ali Mostafa Anwar <ali.mo.anwar@std.agr.cu.edu.eg> Comprehensive R Archive Network (CRAN) Ali Mostafa Anwar [aut, cre], Mohamed Soudy [aut] GPL-3 2019-11-15 application/tgz https://CRAN.R-project.org/package=vhcub doi:10.32614/CRAN.package.vhcub