Estimating mutation and selection coefficients on synonymous
codon bias usage based on models of ribosome overhead cost (ROC).
Multinomial logistic regression and Markov Chain Monte Carlo are used to
estimate and predict protein production rates with/without the presence
of expressions and measurement errors. Work flows with examples for
simulation, estimation and prediction processes are also provided
with parallelization speedup. The whole framework is tested with
yeast genome and gene expression data of Yassour, et al. (2009)
cubfits is an R package providing fits of codon usage bias. For installing cubfits, - see "INSTALL" for detais.