An R package for the calculation and visualisation of codon usage metrics in user-supplied protein-coding sequences, and comparison with those of reference taxa. The package is designed primarily for the analysis of viral open reading frames (ORFs), with the intention of identifying potential host taxa based on overall codon usage similarity, but it can be used for the comparison of any protein-coding input sequence(s).
To install codondiffR, run the following in R:
# install.packages("devtools")
devtools::install_github("adamd3/codondiffR")
A brief run-through of the package is available here.