Fig. 2

Sequence states. a A sequence state in the SID models [21]. Each site (cell) is assigned a residue state (A, T, G or C). b The corresponding extended sequence state in our evolutionary model. Each site is assigned an ancestry index (number) in addition to a residue state. c The corresponding basic sequence state. Each site is assigned an ancestry index alone. The \( \overrightarrow{\omega} \) represents the set of residue states assigned to all sites. The \( \overrightarrow{\upsilon} \) represents the set of ancestry indices assigned to all sites. (Note that the identical symbols (s’s) used in panels a and c represent different types of states (of the same sequence))