Comparisons between various codon substitution models in the concatenating analysis of nDNA.

aIn the models specified with the suffix “-3-”, “-4-”, “-4s-” or “-5-”, three, four or five parameters are optimized with and . The prior probability of each category for the “dG4s” is , and .bThe number of adjustable parameters.cDifferences from the reference state; , , and .dThe average of over all amino acid pairs ; .eThe value parenthesized means that the parameter is fixed at the value specified.fThe scale parameter of a distribution for the variation of mutation rate over time.gThe ratio of double to single and of triple to double nucleotide change exchangeability; .hThe ratio of mean transitional to mean transversional exchangeability; .iThe shape parameter of a discrete gamma distribution for the variation of mutation rate or selective constraint over sites.