In a 2012 Plos One article, we describe a method for classifying effector candidates in filamentous pathogen genomes that relies on probability scores. The rationale behind this scoring and the bits of R code are available through this link.
The original article:
Evolution of codon usage using known mutation frequencies with random direction of mutation
Evolution of codon usage using fixed mutation frequencies and fixed substitution patterns
References for Master
Great papers in biophysics