Codon-substitution models

The states of the model are the 61 sense codons (in the case of the universal genetic code). The Markov process uses a 61x61 rate matrix Q where Qij represents the substitution rate from codon i to j. The model of substitution can be chosen from the "Model of substitution" drop-down list. Three codon-based models are supported:

1.Yang et al. model.
2.An enhancement of the model was suggested by Goldman and Yang.
3.An empirical model.