These substitution models take as argument another substitution model, and add several parameters.
TS98(model={model description}, s1={real>0}, s2={real>0} [, "equilibrium frequencies"])Tuffley and Steel 1998’s ’covarion’ model, taking a nested substitution model as argument for model. The nested model can be any substitution model for any alphabet. See the Bio++ description.
G01(model={model description}, rdist={rate distribution description}, mu={real>0} [, "equilibrium frequencies"])Galtier 2001’s ’covarion’ model, taking a nested substitution model as argument for model and a rate distribution for parameter rdist (see below). The nested model can be any substitution model for any alphabet. See the Bio++ description.
RE08(model={model description}, lambda={real>0}, mu={real>0} [, "equilibrium frequencies"])Rivas and Eddy 2008’s substitution model with gaps, taking a nested substitution model as argument for model. Parameter lambda is the insertion rate, while mu is the deletion rate. See the Bio++ description.