The alignment transducer used to model evolution from the ancestor to the descendent on each branch of the phylogenetic tree. Match, Insert (Ins), and Delete (Del) states represent evolutionary events. States with blue outlines (slow states) have reduced rates of evolution compared to states with red outlines (fast states). The model enters one of the wait states (W1 and W2) when waiting for input from the ancestral sequence.
Satija et al. BMC Evolutionary Biology 2009 9:217 doi:10.1186/1471-2148-9-217