The codonopt package provides methods for sampling from the possible codons of an amino acid sequence and for computing optimality scores for open reading frame sequences.
Installation
You can install the development version of codonopt from GitHub with:
# install.packages("remotes")
remotes::install_github("mfansler/codonopt")Example
This is a basic example which shows how to compute a simple optimality score.
library(codonopt)
score_fraction_optimal(as_codons("AUGUUAGAUUUAUAG"))
#> [1] 0.5