TABLE 1

Definitions of symbols used

SymbolDefinition
dNNumber of nonsynonymous substitutions per nonsynonymous site
dSNumber of synonymous substitutions per synonymous site
ωNonsynonymous/synonymous rate ratio (dN/dS)
κTransition/transversion rate ratio
qEmbedded ImageijRate of transition from codon i to codon j
qEmbedded ImageijRate of transition from nucleotide i to nucleotide j
πjStationary frequency of codon j
μjkStationary frequency of the nucleotide at position k in codon j
ζNucleotide substitution rate multiplier in the noncoding region
nNumber of nucleotide sequences
NNNumber of nucleotides in the noncoding region
NCNumber of codons in the coding region
lLog-likelihood