Table 2.

Model Configurations Used in the Experiments.

g1	One instance of M0; codon frequencies estimated from whole MSA with a F3X4 model
g2	Two instances of M0; codon frequencies estimated from whole MSA
2	Two instances of M0; codon frequencies estimated from either tandem regions or rest of the MSA, respectively (which leads to two different sets of frequencies)
rg2	Two instances of M0; codon frequencies estimated from whole MSA. Different model mutation rates assumed
r2	Two instances of M0; codon frequencies estimated from either tandem regions or rest of the MSA. Different model mutation rates assumed.