With this option, you can choose the general attributes of the substitution models for DNA and protein sequence evolution.
Substitutions Type
Here you may select a substitutions type of Nucleotide, Syn-Nonsynonymous, or Amino Acid. The selection in this row affects the available models in the model row.
Model
You can select a stochastic model for estimating evolutionary distances by clicking on the row then selecting a model for the current Substitutions Type.
Transition/Transversion Ratio
This option will be visible if the chosen model requires you to provide a value for the Transition/Transversion ratio (R).
Pattern among Lineages
This option becomes available if the distance model you have selected has formulas that allow the relaxation of the assumption of homogeneity of substitution patterns among lineages.
Rates among Sites
This option becomes available if the distance model you have selected has formulas that allow rate variation among sites. If you choose gamma distributed rates, then the Gamma parameter option becomes visible.