Model parameters file content

The content of this file is highly dependant on the substitution model used and we cannot describe it in general terms. The fields used to assign a value to each parameter are hopefully quite self-explanatory as long as you know the underlying substitution model. You might need to have a look at the transition matrices section to understand the PHASE concept of ``rate ratios'' in substitution models. Each ``Rate ratio i'' parameter in this file stands for the parameter $\alpha_i$ in the transition matrix of the corresponding model. Transition matrices for all implemented substitution models are given there for DNA models and there for RNA models.