# Applying a time-reversible codon model

We display the full set of codon models available.

## Using the conditional nucleotide form codon model

The CNFGTR model (Yap et al) is the most robust of the time-reversible codon models available (Kaehler et al). By default, this model does not optimise the codon frequencies but uses the average estimated from the alignment. We configure the model to optimise the root motif probabilities.

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Applying GNC, a non-stationary codon model

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Testing hypotheses about sequence evolution