Table 1 Substitution rate matrix Q for the unrestricted model of nucleotide substitutions (UNREST). The diagonals of Q are determined by the requirement that each row sum to zero
ATGC
AEmbedded ImageEmbedded ImageEmbedded Image
TEmbedded ImageEmbedded ImageEmbedded Image
GEmbedded ImageEmbedded ImageEmbedded Image
CEmbedded ImageEmbedded ImageEmbedded Image
  • The nucleotide stationary distribution Embedded Image is given by the set of equations Embedded Image under the constraint Embedded Image