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().


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1.0.0 by Ali Mostafa Anwar, 20 days ago

Browse source code at

Authors: Ali Mostafa Anwar [aut, cre] , Mohamed Soudy [aut]

Documentation:   PDF Manual  

GPL-3 license

Imports Biostrings, coRdon, ggplot2, seqinr, stringr

Suggests testthat

See at CRAN