Codon-usage bias: unequal codon frequencies in a gene.

Nonsynonymous substitution: a nucleotide substitution that changes the encoded amino acid.

Prior probability: the probability of an event (such as a site belonging to a site class) before the collection of data.

Positive selection: darwinian selection fixing advantageous mutations with positive selective coefficients. The term is used interchangeably with molecular adaptation and adaptive molecular evolution.

Posterior probability: the probability of an event conditional on the observed data, which reflects both the prior assumption and information in the data.

Purifying selection: natural selection against deleterious mutations with negative selective coefficients. The term is used interchangeably with negative selection or selective constraints.

Synonymous substitution: a nucleotide substitution that does not change the encoded amino acid.

Transition/transversion rate bias: unequal substitution rates between nucleotides, with a higher rate for transitions (changes between T and C and between A and G) than transversions (all other changes).