Fig. 4.

Update motif instances at the leaves. We update the motif instance for each species in the current ortholog group, one by one. For each species, the probability that a motif instance starts at each position is calculated. All those probabilities, together with the probability that there is no motif instance in the gene, are used. The sampler will randomly decide whether there is a motif instance and where it is if there is one, according to those probabilities. Note that only the ancestral motif instance that is underlined in the figure contributes to the updating of the motif instance in the current species. If there is a motif instance sampled, the two nucleotides on the left and the right of the motif instance are recorded for future use to decide the motif width.